Query 018129
Match_columns 360
No_of_seqs 302 out of 1063
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 06:23:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018129.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018129hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1554 COP9 signalosome, subu 100.0 4.3E-96 9E-101 687.6 23.4 342 2-359 5-346 (347)
2 cd08069 MPN_RPN11_CSN5 Mov34/M 100.0 6.4E-59 1.4E-63 445.2 26.7 262 52-323 1-267 (268)
3 cd08065 MPN_eIF3h Mpr1p, Pad1p 100.0 1.7E-42 3.6E-47 331.6 22.0 219 61-286 1-228 (266)
4 KOG1560 Translation initiation 100.0 1.4E-35 3.1E-40 278.6 13.2 222 57-285 9-248 (339)
5 cd08064 MPN_eIF3f Mpr1p, Pad1p 100.0 7E-32 1.5E-36 258.1 24.2 245 63-338 1-247 (265)
6 cd08067 MPN_2A_DUB Mov34/MPN/P 100.0 6.2E-31 1.3E-35 239.9 17.4 133 62-200 6-148 (187)
7 cd08062 MPN_RPN7_8 Mpr1p, Pad1 100.0 7.1E-28 1.5E-32 232.3 22.7 201 61-288 1-205 (280)
8 cd08058 MPN_euk_mb Mpr1p, Pad1 100.0 1.2E-28 2.7E-33 208.7 12.6 113 69-197 2-119 (119)
9 cd08068 MPN_BRCC36 Mov34/MPN/P 100.0 1.1E-27 2.4E-32 226.0 16.5 138 60-199 1-152 (244)
10 PF01398 JAB: JAB1/Mov34/MPN/P 99.9 3.9E-27 8.4E-32 197.2 11.7 112 59-172 2-114 (114)
11 smart00232 JAB_MPN JAB/MPN dom 99.9 3.8E-26 8.2E-31 194.2 17.9 134 62-198 1-134 (135)
12 cd08057 MPN_euk_non_mb Mpr1p, 99.9 1.9E-26 4.1E-31 204.3 16.1 134 63-199 1-137 (157)
13 KOG1555 26S proteasome regulat 99.9 4.8E-26 1E-30 219.7 14.9 192 60-256 30-236 (316)
14 KOG2975 Translation initiation 99.9 1.4E-25 3E-30 210.0 15.5 195 61-285 21-218 (288)
15 PLN03246 26S proteasome regula 99.9 1.3E-24 2.8E-29 211.6 22.2 203 56-286 1-209 (303)
16 cd08063 MPN_CSN6 Mpr1p, Pad1p 99.9 8.7E-24 1.9E-28 204.6 20.7 201 62-288 2-209 (288)
17 cd08066 MPN_AMSH_like Mov34/MP 99.9 8.8E-24 1.9E-28 190.8 17.2 131 60-203 1-134 (173)
18 cd07767 MPN Mpr1p, Pad1p N-ter 99.9 2.6E-22 5.5E-27 166.9 13.3 115 71-194 2-116 (116)
19 cd08070 MPN_like Mpr1p, Pad1p 99.8 2.4E-18 5.3E-23 147.4 14.1 119 68-198 2-120 (128)
20 KOG1556 26S proteasome regulat 99.8 7.9E-18 1.7E-22 156.8 14.4 166 58-252 6-179 (309)
21 COG1310 Predicted metal-depend 99.6 1.9E-14 4E-19 124.4 11.3 104 63-179 2-105 (134)
22 cd08072 MPN_archaeal Mov34/MPN 99.5 8.4E-14 1.8E-18 118.2 12.1 108 65-197 1-108 (117)
23 KOG2880 SMAD6 interacting prot 99.5 2E-14 4.4E-19 140.1 6.4 131 56-199 247-379 (424)
24 cd08073 MPN_NLPC_P60 Mpr1p, Pa 99.4 1E-12 2.2E-17 110.2 11.6 94 69-180 2-95 (108)
25 cd08060 MPN_UPF0172 Mov34/MPN/ 99.3 3.7E-11 8E-16 109.6 13.1 110 65-182 1-114 (182)
26 PF14464 Prok-JAB: Prokaryotic 99.3 1.9E-11 4.1E-16 100.1 8.7 95 67-180 2-96 (104)
27 cd08056 MPN_PRP8 Mpr1p, Pad1p 99.2 3.9E-10 8.4E-15 107.4 12.9 126 62-202 37-170 (252)
28 cd08059 MPN_prok_mb Mpr1p, Pad 98.9 1.1E-08 2.4E-13 83.9 10.0 91 69-180 2-92 (101)
29 TIGR02256 ICE_VC0181 integrati 98.9 2.8E-08 6.1E-13 86.2 12.3 109 70-179 2-113 (131)
30 TIGR03735 PRTRC_A PRTRC system 98.7 2.6E-08 5.5E-13 91.5 7.7 112 64-200 74-186 (192)
31 KOG3050 COP9 signalosome, subu 98.5 2.5E-07 5.3E-12 87.1 6.6 160 62-250 10-176 (299)
32 PF03665 UPF0172: Uncharacteri 98.4 8.7E-06 1.9E-10 75.3 13.8 114 62-182 3-120 (196)
33 cd08061 MPN_NPL4 Mov34/MPN/PAD 98.3 3E-05 6.5E-10 75.2 15.6 136 58-200 8-161 (274)
34 KOG3289 Uncharacterized conser 97.5 0.0016 3.6E-08 59.1 12.1 114 62-181 3-119 (199)
35 PF05021 NPL4: NPL4 family; I 97.4 0.0026 5.7E-08 62.7 12.5 108 86-200 2-144 (306)
36 KOG1795 U5 snRNP spliceosome s 83.0 3.1 6.7E-05 48.1 6.9 110 80-202 2112-2225(2321)
37 KOG2834 Nuclear pore complex, 61.8 1E+02 0.0022 32.5 11.2 132 60-199 174-341 (510)
38 cd08071 MPN_DUF2466 Mov34/MPN/ 40.0 2.2E+02 0.0048 23.8 9.7 25 138-162 59-83 (113)
39 PF14220 DUF4329: Domain of un 31.7 41 0.0009 29.0 2.6 65 80-162 18-87 (123)
40 PF14778 ODR4-like: Olfactory 30.9 78 0.0017 32.0 4.8 61 87-150 1-74 (362)
41 COG5178 PRP8 U5 snRNP spliceos 30.8 67 0.0015 37.7 4.6 109 80-202 2151-2265(2365)
42 COG1029 FwdB Formylmethanofura 30.6 1.6E+02 0.0034 30.4 6.8 57 135-198 138-202 (429)
43 PF15659 Toxin-JAB1: JAB-like 26.7 70 0.0015 29.0 3.3 27 135-162 112-138 (162)
44 PF04002 RadC: RadC-like JAB d 26.0 4E+02 0.0087 22.4 9.0 83 67-162 5-88 (123)
45 PF06442 DHFR_2: R67 dihydrofo 25.4 36 0.00078 26.4 1.0 11 139-149 40-50 (78)
No 1
>KOG1554 consensus COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=100.00 E-value=4.3e-96 Score=687.57 Aligned_cols=342 Identities=73% Similarity=1.134 Sum_probs=323.7
Q ss_pred chhhhhhhhhhcccceecCCCCCCCCCCCCCCcccccCChHhhhHHHhcCCCCCCCCCeeEEEECHHHHHHHHHHHhcCC
Q 018129 2 DSSIAQKTWELENNIVSMETPPTNSTADTSASDAIFFYDEGAQTKFQQEKPWVNDPHYFKRVKISALALLKMVVHARSGG 81 (360)
Q Consensus 2 ~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~d~~~~~d~~~~~~~~~~~pw~~~p~~~~~V~Is~~vLlkIl~Ha~~~~ 81 (360)
++.+|+++||++|||+.+++. |.+|+||.+.+.++..++||..||++|+.|+|++++|+||++||++|+
T Consensus 5 ~s~~~~k~we~en~~~~~~~~-----------deif~yd~~sq~~~~~~kpw~~Dp~~fk~vkISalAllKm~~hA~~Gg 73 (347)
T KOG1554|consen 5 SSYTAQKTWELENNIQSVESE-----------DEIFRYDQKSQRKIILEKPWSTDPHYFKHVKISALALLKMVMHARSGG 73 (347)
T ss_pred cccchhHHHHHhhhhccCccc-----------hhhhhcCHHHHHHHHhcCcccCCCchhhhhhhHHHHHHHHHHHHhcCC
Confidence 456899999999999999875 999999999999999999999999999999999999999999999999
Q ss_pred CceeEEEeeeEecCCeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCCCCceEEEEecCCCCCCccCHHhHH
Q 018129 82 TIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAVGWYHSHPGYGCWLSGIDVS 161 (360)
Q Consensus 82 p~EV~GlLLG~~~~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~~e~vVGWYHSHP~~g~~~S~iDI~ 161 (360)
+.||||+|+|+.++++++|+|||++|++|||+|||++.+++|||..+.+.++.+||.+++||||||||+||||+|+|||.
T Consensus 74 nlEiMGlm~Gkv~g~t~IvmD~FaLPVeGTETRVNAq~~AyEYmv~Y~e~~k~~gr~envVGWyHSHPgYgCWLSgIDVs 153 (347)
T KOG1554|consen 74 NLEIMGLMQGKVDGDTIIVMDSFALPVEGTETRVNAQAEAYEYMVQYIEEAKNVGRLENVVGWYHSHPGYGCWLSGIDVS 153 (347)
T ss_pred CeEEEeeecccccCCeEEEEeccccccccccceechHHHHHHHHHHHHHHHHHhhhhhceeeeeecCCCCCccccCcchh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCCCCCCCCCCCcccccchhhhhhhcCccceeEEeeEEEecChh
Q 018129 162 TQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEGYKPPDEPISEYQTIPLNKIEDFGVHCKQYYSLDITYFKSSL 241 (360)
Q Consensus 162 tQ~~yQ~~~~p~V~LVvDp~~t~~~G~v~ikAFRl~p~~~~~~~~~~~e~~~ip~~ki~d~g~~~~~fyeLpV~i~~s~l 241 (360)
||..+|++++||||+||||.||++.|++.|+|||+||.||+++.+++++|+.+|++||+|||+||.+||+|+|++|++.+
T Consensus 154 TQ~lNQ~fQePfvAvViDP~Rtlsagkv~iGAFRTyp~gyk~~d~~~seyqtipl~kied~gvHck~yysl~isyfks~l 233 (347)
T KOG1554|consen 154 TQMLNQRFQEPFVAVVIDPTRTLSAGKVNIGAFRTYPKGYKPPDEPPSEYQTIPLNKIEDFGVHCKQYYSLEISYFKSSL 233 (347)
T ss_pred HHHHhhhhcCCeEEEEecCccccccCceeeceeecccCCCCCCCCCchhhhccchhhhhhcccceEEeeccchhhhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhccccccccCCCCCccChHHHHHHHHHHHHHHHHHHHhhccCCCCCCCCCCCCCcchhhHHHHHHhhHhhHH
Q 018129 242 DCHLLDLLWNKYWVNTLSSSPLLGNGDYVAGQISDLAEKLEQAENQLSHSRYGPLIAPPPRRKEEDSQLAKITRDSAKIT 321 (360)
Q Consensus 242 ~~~~L~~L~~~~w~~~Ls~s~ll~n~~~l~~~i~dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 321 (360)
+.++|+.||++||+++|+++|+++|.+|+.+||.||++|+.+.+.++.++. ....++..++.+|+|+++|++++.
T Consensus 234 d~kll~~Lwnkywv~Tlsss~ll~N~dy~~~qi~d~~ekl~q~~~~l~~s~-----~~~d~~~ed~~~l~k~~~Ds~~~~ 308 (347)
T KOG1554|consen 234 DMKLLELLWNKYWVRTLSSSPLLKNIDYLNGQIRDLSEKLEQREDSLETSD-----NTHDRKSEDENLLAKATRDSSKCT 308 (347)
T ss_pred hHHHHHHHHhhhhhcccccccccccchhhcchhhhHHHHHHhhhhhcccCc-----ccccccccchhhhhhhhhhhhhhh
Confidence 999999999999999999999999999999999999999999999987651 111233456678999999999999
Q ss_pred HHHHHhHHHHHHHHHhcCCCCCCCcCCCCCCCCCCCCC
Q 018129 322 VEQVHGLMSQVIKDILFNSVRQSTKTHAEPSDPEPMIE 359 (360)
Q Consensus 322 ~e~~~g~~~~~~k~~~f~~~~~~~~~~~~~~~~~~~~~ 359 (360)
.|+.||+|+|++|++||+....+++...++..+.+|+.
T Consensus 309 ~e~~~gl~s~vvkd~lf~~~~~~~k~~~~s~~~~~di~ 346 (347)
T KOG1554|consen 309 NELIHGLMSQVVKDKLFNDNFHSSKRMNSSQERCHDIG 346 (347)
T ss_pred hcchhHHHHHHHHHHHHHhhccccCCCCcCCCCCcccc
Confidence 99999999999999999998776677777777777653
No 2
>cd08069 MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5. This family contains proteasomal regulatory protein Rpn11 (26S proteasome regulatory subunit rpn11; PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the 19S-proteasome; regulatory particle number 11) and signalosomal CSN5 (COP9 signalosome complex subunit 5; COP9 complex homolog subunit 5; c-Jun activation domain-binding protein-1; CSN5/JAB1; JAB1). COP9 signalosome (CSN) and the proteasome lid are paralogous complexes and their respective subunits CSN5 and Rpn11 are most closely related between the two complexes, both containing the conserved JAMM (JAB1/MPN/Mov34 metalloenzyme) motif involved in zinc ion coordination and providing the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology; mutations i
Probab=100.00 E-value=6.4e-59 Score=445.16 Aligned_cols=262 Identities=64% Similarity=0.991 Sum_probs=234.3
Q ss_pred CCCCCCCCeeEEEECHHHHHHHHHHHhcCCCceeEEEeeeEecCCeEEEEEEEeCCcccCCCccccccChHHHHHHHHH-
Q 018129 52 PWVNDPHYFKRVKISALALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQ- 130 (360)
Q Consensus 52 pw~~~p~~~~~V~Is~~vLlkIl~Ha~~~~p~EV~GlLLG~~~~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~- 130 (360)
||+.+|++|++|+|+++|+++|++||+++.|.||||+|+|.+++++++|++||++|+.++++++++.. +|+..|++
T Consensus 1 ~~~~~~~~~~~V~Is~~allkil~Ha~~~~p~Ev~GlLlG~~~~~~v~Vt~~fp~p~~~t~~~v~~~~---e~~~~m~~~ 77 (268)
T cd08069 1 PWKPDPDYFEKVYISSLALLKMLKHARAGGPIEVMGLMLGKVDDYTIIVVDVFALPVEGTETRVNAQD---EFQEYMVQY 77 (268)
T ss_pred CCCCCCCcccEEEECHHHHHHHHHHHhccCCceEEEEEEeeecCCeEEEEEEEECCcCCCCCceeccH---HHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999888755 45666666
Q ss_pred -HHHHhCCCCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCCCCC--CCCC
Q 018129 131 -TNKQAGRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEGYKP--PDEP 207 (360)
Q Consensus 131 -~~r~v~~~e~vVGWYHSHP~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~t~~~G~v~ikAFRl~p~~~~~--~~~~ 207 (360)
+++++++++++||||||||++|||||++||++|..||++.+|+|+|||||.++.++|++.|+|||++|.++.+ +...
T Consensus 78 ~~~~~~~~~~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~~~~V~lViDP~~t~~~g~~~i~Afr~~~~~~~~~~~~~~ 157 (268)
T cd08069 78 EMLKQTGRPENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDPIRSLVKGKVVIGAFRTIPPGYKPLEPRQT 157 (268)
T ss_pred HHHHHhCCCceeEeeeccCCCcCCcCCHHHHHHHHHHHhcCCCcEEEEEeCCccccCCcceeeEEEEECccccccCcccC
Confidence 9999999999999999999999999999999999999999999999999999867899999999999999885 4445
Q ss_pred CCcccccchhhhhhhcCccceeEEeeEEEecChhHHHHHHHHhccccccccCCCCCccCh-HHHHHHHHHHHHHHHHHHH
Q 018129 208 ISEYQTIPLNKIEDFGVHCKQYYSLDITYFKSSLDCHLLDLLWNKYWVNTLSSSPLLGNG-DYVAGQISDLAEKLEQAEN 286 (360)
Q Consensus 208 ~~e~~~ip~~ki~d~g~~~~~fyeLpV~i~~s~l~~~~L~~L~~~~w~~~Ls~s~ll~n~-~~l~~~i~dl~~~~~~~~~ 286 (360)
.++++.+|.+++++++.++++||+|||+|+++.+++.+|..||++||+.+|+.+++.+|. ++..++|.+|++++.++..
T Consensus 158 ~s~~~~~~~~~~~~~~~~~~~y~~l~i~~~~s~l~~~~L~~l~~~~w~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 237 (268)
T cd08069 158 TSNIGHLPKPKIEDFGGHNKQYYSLPIEYFKSSLDRKLLLNLWNKYWVNTLSLSPLLENSNEYTIKQILDLAEKLEKAEQ 237 (268)
T ss_pred ccccCccCcHHHHHhCchhcEEEEeeeEEecCHHHHHHHHHHHHHhHHHHhhCCchhhhhhHHHHHHHHHHHHHHHHHHh
Confidence 567788999999999999999999999999999999999999999999999999999998 9999999999999999887
Q ss_pred hhccCCCCCCCCCCCCCcchhhHHHHHHhhHhhHHHH
Q 018129 287 QLSHSRYGPLIAPPPRRKEEDSQLAKITRDSAKITVE 323 (360)
Q Consensus 287 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e 323 (360)
...+.. +.....+...++.|+ +|+.++++|
T Consensus 238 ~~~~~~------~~~~~~~~~~~~~~~-~~~~~~~~~ 267 (268)
T cd08069 238 QEERLT------GEELDIANVGKLDKA-RDSSKIHLE 267 (268)
T ss_pred hhhccC------hhhhcccchhhhhhc-cccchhhhc
Confidence 765420 111123345566766 888888776
No 3
>cd08065 MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF2h. Eukaryotic translation initiation factor 3 (eIF3) subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma; eIF3-p40) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity.Together with eIF3e and eIF3f, eIF3h stabilizes the eIF3 complex. Results suggest that eIF3h regulates cell growth and viability, and that over-expression of the gene may provide growth advantage to prostate, breast, and liver cancer cells. For example, EIF3h gene amplification is common in late-stage prostate cancer suggesting that it may be functionally involved in the progression of the disease. It has been shown that coamplification of MYC, a well characterized oncogene involved in cell growth, different
Probab=100.00 E-value=1.7e-42 Score=331.60 Aligned_cols=219 Identities=21% Similarity=0.307 Sum_probs=189.5
Q ss_pred eEEEECHHHHHHHHHHHhcCCCceeEEEeeeEecCCeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCCCCc
Q 018129 61 KRVKISALALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLEN 140 (360)
Q Consensus 61 ~~V~Is~~vLlkIl~Ha~~~~p~EV~GlLLG~~~~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~~e~ 140 (360)
++|.|+++|+++|++||+++.|.+|||+|||...+++++||||||+|+.++++...+.....+|+.+|+++++++|.+++
T Consensus 1 ~~V~I~~~vllkIv~H~~~~~p~~v~G~LLG~~~~~~leVtn~Fp~P~~~~~~~~~~~~~~~~yq~~m~~~~r~v~~~e~ 80 (266)
T cd08065 1 TSVQIDGLVVLKIIKHCKEELPELVQGQLLGLDVGGTLEVTNCFPFPKSEEDDSDRADEDIADYQLEMMRLLREVNVDHN 80 (266)
T ss_pred CEEEEeHHHHHHHHHHHhcCCCcEEEEEEeeeEcCCEEEEEeccCCCCCCCCCcchhhhhHHHHHHHHHHHHHHhCCCCc
Confidence 47999999999999999999999999999999999999999999999987765533333456899999999999999999
Q ss_pred eEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCCCCCCCCCCCcccccchhhhh
Q 018129 141 AVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEGYKPPDEPISEYQTIPLNKIE 220 (360)
Q Consensus 141 vVGWYHSHP~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~t~~~G~v~ikAFRl~p~~~~~~~~~~~e~~~ip~~ki~ 220 (360)
+|||||||| +|+|.+..+|++|+.||...+++|+||+||.++ ..|++.++|||++|.+....++ ..+....++
T Consensus 81 iVGWY~S~p-~~~~~~~s~id~~~~~q~~~~~~v~Li~D~~~s-~~g~l~lkAyrl~~~~~~~~~~-----~~~~~~~l~ 153 (266)
T cd08065 81 HVGWYQSTY-LGSFFTRDLIETQYNYQEAIEESVVLVYDPSKT-SQGSLSLKAYRLSEKFMELYKE-----GKFSTESLR 153 (266)
T ss_pred EEEeEeecC-CCCcCCHHHHHHHHHHhccCCCCEEEEECCCcc-cccceeeEEEEEcHHHHHHhhc-----CCcCHHHHH
Confidence 999999999 999999999999999999888999999999985 4788999999999876422111 234445566
Q ss_pred hhc-CccceeEEeeEEEecChhHHHHHHHHh-------ccccccccCCCCCc-cChHHHHHHHHHHHHHHHHHHH
Q 018129 221 DFG-VHCKQYYSLDITYFKSSLDCHLLDLLW-------NKYWVNTLSSSPLL-GNGDYVAGQISDLAEKLEQAEN 286 (360)
Q Consensus 221 d~g-~~~~~fyeLpV~i~~s~l~~~~L~~L~-------~~~w~~~Ls~s~ll-~n~~~l~~~i~dl~~~~~~~~~ 286 (360)
..+ .+.++|+||||+|+++.|++.+|..|. ..|..++|+..+++ +|++.++++||+|++++.++..
T Consensus 154 ~~~~~~~~if~eiPv~i~n~~l~~~~L~~l~~~~~~~~~~~~~l~l~~~~~le~~l~~l~~~id~l~~e~~~~~~ 228 (266)
T cd08065 154 EANLTFSNIFEEIPVVIRNSHLVNALLSELEEDSPSSQSDFDRLDLSTNSFLEKNLELLMESVDELSQEQGKFNY 228 (266)
T ss_pred HhcCchhcEEEEEEEEEEchHHHHHHHHhcccCCCcccCCcccccccCchhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 666 578999999999999999999999995 34778999999988 8999999999999999887653
No 4
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.4e-35 Score=278.57 Aligned_cols=222 Identities=21% Similarity=0.287 Sum_probs=185.3
Q ss_pred CCCeeEEEECHHHHHHHHHHHhcCCCc--eeEEEeeeEecCCeEEEEEEEeCCccc--CCCccccc-cCh--HHHHHHHH
Q 018129 57 PHYFKRVKISALALLKMVVHARSGGTI--EVMGLMQGKTDGDAIIVMDAFALPVEG--TETRVNAQ-ADA--YEYMVDYS 129 (360)
Q Consensus 57 p~~~~~V~Is~~vLlkIl~Ha~~~~p~--EV~GlLLG~~~~~~leVtd~F~lP~~~--te~~v~~~-~e~--~ey~~~ml 129 (360)
..++++|.|+++|++||++||++..+. -+.|.|+|.+.+++++||||||+|... .++.++.+ .+. ..||.+|+
T Consensus 9 ~p~vk~v~ldsLvVMkiiKHc~ee~~n~d~~~GvL~Glvvd~~LeITncFp~p~~~~~edda~~~~~~de~rq~~~l~ml 88 (339)
T KOG1560|consen 9 SPPVKRVELDSLVVMKIIKHCREEFPNGDGTQGVLLGLVVDGRLEITNCFPFPSVLENEDDAVNKSVSDEARQAYQLAML 88 (339)
T ss_pred CCccceeeehhHHHHHHHHHHHhhcCCcchhhheeeeeeecceeEeecccCCCccCCCccchhhhhhhHHHHHHHHHHHH
Confidence 347999999999999999999987664 677999999999999999999999732 23333332 222 36899999
Q ss_pred HHHHHhCCCCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCCCCCCCCCCC
Q 018129 130 QTNKQAGRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEGYKPPDEPIS 209 (360)
Q Consensus 130 ~~~r~v~~~e~vVGWYHSHP~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~t~~~G~v~ikAFRl~p~~~~~~~~~~~ 209 (360)
+.+|.+|.+...||||+||. +|.|+|...+++|+.||.+.|+.|++|+||.++ ++|.+.+||||++|+....-++
T Consensus 89 rrlr~vnid~~hVGwYqs~~-vgs~lS~~lveSqy~YQ~a~pesVvliYD~~ks-sqG~L~lrAyrLTp~am~~~ke--- 163 (339)
T KOG1560|consen 89 RRLRYVNIDHLHVGWYQSAY-VGSFLSPALVESQYAYQKAIPESVVLIYDPIKS-SQGTLSLRAYRLTPEAMAAHKE--- 163 (339)
T ss_pred HHhhhcCccceeeeeeeeeh-hccccCHHHHHHHHHHHhcCCccEEEEeccccc-cCceEEeehhhcCHHHHHHHhc---
Confidence 99999999999999999999 899999999999999999999999999999998 4999999999999975321111
Q ss_pred cccccchhhhhhhc-CccceeEEeeEEEecChhHHHHHHHHh-------cc--ccccccCCCCCc-cChHHHHHHHHHHH
Q 018129 210 EYQTIPLNKIEDFG-VHCKQYYSLDITYFKSSLDCHLLDLLW-------NK--YWVNTLSSSPLL-GNGDYVAGQISDLA 278 (360)
Q Consensus 210 e~~~ip~~ki~d~g-~~~~~fyeLpV~i~~s~l~~~~L~~L~-------~~--~w~~~Ls~s~ll-~n~~~l~~~i~dl~ 278 (360)
..+..+.++..| ++.+.|.||||.|++|+|.+.++.+|. ++ +-..+|++..-+ +|++.|++.+|+|.
T Consensus 164 --kdwtpealk~~nltyenmfeElPIVIknS~L~nvlmseLs~~e~c~sdk~~~~~fdlgs~t~leknir~lme~vDEl~ 241 (339)
T KOG1560|consen 164 --KDWTPEALKSANLTYENMFEELPIVIKNSHLANVLMSELSEPEDCESDKPLHSNFDLGSGTRLEKNIRLLMERVDELH 241 (339)
T ss_pred --CCCCHHHHHhcCCCHHHHHhhcCeeeeccHHHHHHHHhccccccccccccccccccccchhhHHHHHHHHHHHHHHHH
Confidence 245667778788 589999999999999999999999997 12 245667676656 89999999999999
Q ss_pred HHHHHHH
Q 018129 279 EKLEQAE 285 (360)
Q Consensus 279 ~~~~~~~ 285 (360)
+++.++.
T Consensus 242 qe~~~l~ 248 (339)
T KOG1560|consen 242 QEIVNLN 248 (339)
T ss_pred HHHHHHH
Confidence 9885544
No 5
>cd08064 MPN_eIF3f Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF3f. Eukaryotic translation initiation factor 3 (eIF3) subunit F (eIF3F; EIF3S5; eIF3-p47; eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa; Mov34/MPN/PAD-1 family protein) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity. It has been shown that eIF3f mRNA expression is significantly decreased in many human tumors including pancreatic cancer and melanoma. EIF3f is a potent inhibitor of HIV-1 replication; it mediates restriction of HIV-1 expression through several factors including the serine/arginine-rich (SR) protein 9G8, and cyclin-dependent kinase 11 (CDK11). EIF3f phosphorylation by CDK11 is important in regulating its function in translation and ap
Probab=100.00 E-value=7e-32 Score=258.11 Aligned_cols=245 Identities=17% Similarity=0.274 Sum_probs=195.6
Q ss_pred EEECHHHHHHHHHHHhc--CCCceeEEEeeeEecCCeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCCCCc
Q 018129 63 VKISALALLKMVVHARS--GGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLEN 140 (360)
Q Consensus 63 V~Is~~vLlkIl~Ha~~--~~p~EV~GlLLG~~~~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~~e~ 140 (360)
|+|||+|+++|++|+.+ ..+.+|+|.|||...+++++|||||++|+..+++++..+ .+|+.+|+++++++++++.
T Consensus 1 v~ihPlVll~I~dH~~R~~~~~~~V~G~LLG~~~~~~veItnsF~~p~~~~~~~~~~d---~~y~~~m~~~~kkv~~~~~ 77 (265)
T cd08064 1 VRVHPVVLFSILDSYERRNEGQERVIGTLLGTRSEGEVEITNCFAVPHNESEDQVAVD---MEYHRTMYELHQKVNPKEV 77 (265)
T ss_pred CEEccHHHHhHHHHHhhhcCCCcEEEEEEEEEEeCCEEEEEeCeecceeCCCCeEEEc---HHHHHHHHHHHHHhCCCCc
Confidence 68999999999999864 678999999999999999999999999998777766554 3799999999999999999
Q ss_pred eEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCCCCCCCCCCCcccccchhhhh
Q 018129 141 AVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEGYKPPDEPISEYQTIPLNKIE 220 (360)
Q Consensus 141 vVGWYHSHP~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~t~~~G~v~ikAFRl~p~~~~~~~~~~~e~~~ip~~ki~ 220 (360)
+||||||||... .+...|+.|+.+|...+++|+|++||..+ .+++.++||++.+.+....
T Consensus 78 vVGWY~tg~~~~--~~~~~Ih~~~~~~~~~~~pI~L~~D~~~~--~~~l~i~ay~~~~~~~~~~---------------- 137 (265)
T cd08064 78 IVGWYATGSEIT--EHSALIHDYYSRECTSYNPIHLTVDTSLD--DGKMSIKAYVSSPLGVPGK---------------- 137 (265)
T ss_pred EEeeeeCCCCCC--ccHHHHHHHHHhhCCCCCCEEEEEeCCCC--CCCcceEEEEEEecccCCC----------------
Confidence 999999999533 34556666666654434789999999875 4689999999998653211
Q ss_pred hhcCccceeEEeeEEEecChhHHHHHHHHhccccccccCCCCCccChHHHHHHHHHHHHHHHHHHHhhccCCCCCCCCCC
Q 018129 221 DFGVHCKQYYSLDITYFKSSLDCHLLDLLWNKYWVNTLSSSPLLGNGDYVAGQISDLAEKLEQAENQLSHSRYGPLIAPP 300 (360)
Q Consensus 221 d~g~~~~~fyeLpV~i~~s~l~~~~L~~L~~~~w~~~Ls~s~ll~n~~~l~~~i~dl~~~~~~~~~~~~~~~~~~~~~~~ 300 (360)
....+|.+||+++.++..|+..++.|++..|..+ ...++.++++++.+++..|..+++++..-+..-..|. .+
T Consensus 138 ---~~~~~F~~ip~~i~~~eaE~i~v~~l~~~~~~~~-~~~~~~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~g~--~~- 210 (265)
T cd08064 138 ---TLGSMFVPIPLELLYSEAERVALDLLAKTLASPS-RSAPLTSDLEQLEASLEKLQEMLDRVLRYVEDVLAGK--VK- 210 (265)
T ss_pred ---CcceEEEEcceeeecCcHHHHHHHHHHhhccCCc-ccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHcCC--CC-
Confidence 2458999999999999999999999999999887 5556669999999999999999988876664321111 00
Q ss_pred CCCcchhhHHHHHHhhHhhHHHHHHHhHHHHHHHHHhc
Q 018129 301 PRRKEEDSQLAKITRDSAKITVEQVHGLMSQVIKDILF 338 (360)
Q Consensus 301 ~~~~~~~~~~~~~~~~~~~~~~e~~~g~~~~~~k~~~f 338 (360)
...+-...|.+++...-++..|+-.+.+...+++.|+
T Consensus 211 -~d~~i~r~l~~~~~~lp~~~~~~f~~~~~~~~~D~lm 247 (265)
T cd08064 211 -ADNAIGRYLMDALTSVPKLDPEEFEKMFNSSLQDLLM 247 (265)
T ss_pred -CCHHHHHHHHHHHhhCCCCCHHHHHHHHHhhcchHHH
Confidence 1122345577778777788888888888888888776
No 6
>cd08067 MPN_2A_DUB Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase. This family includes histone H2A deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases (DUBs), with possible Zn2+-dependent ubiquitin isopeptidase activity. It contains the SWIRM (Swi3p, Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR, TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain can bind directly to DNA. 2A-DUB is specific for monoubiquitinated H2A (uH2A), regulating transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. 2A-DUB interacts with p/CAF (p300/CBP-associated factor) in a co-regulatory protein complex, where the status of acetylation of nucleosomal histones modulates its deubiquitinase activity. 2A-DUB is a positive regulator of androgen receptor (AR) transactivation activity on a reporter gene; it p
Probab=99.97 E-value=6.2e-31 Score=239.94 Aligned_cols=133 Identities=26% Similarity=0.372 Sum_probs=115.7
Q ss_pred EEEECHHHHHHHHHHHhcCCCceeEEEeeeEec--CCeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCCCC
Q 018129 62 RVKISALALLKMVVHARSGGTIEVMGLMQGKTD--GDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLE 139 (360)
Q Consensus 62 ~V~Is~~vLlkIl~Ha~~~~p~EV~GlLLG~~~--~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~~e 139 (360)
+|+|++.||+||++||+.+. .||||+|+|..+ ++.++|+++|++|+..++++++++ + +++.+|++.+++.| +
T Consensus 6 ~V~Is~~all~m~~Ha~~~~-~EvcGlL~G~~d~~~~~l~Vt~~~p~~~~~~~~~~e~d--p-~~q~e~~~~l~~~g--l 79 (187)
T cd08067 6 KVTVSSNALLLMDFHCHLTT-SEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLDCEMD--P-VSETEIRESLESRG--L 79 (187)
T ss_pred EEEECHHHHHHHHHHhcCCC-cEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCcccccC--H-HHHHHHHHHHHHcC--C
Confidence 79999999999999999987 999999999976 467999999999998777777664 3 56888999998654 7
Q ss_pred ceEEEEecCCCCCCccCHHhHHHHHhhhhcCC-------CeEEEEEcCCCCccC-CeeeEEEEEEccCC
Q 018129 140 NAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQE-------PFLAVVIDPTRTVSA-GKVEIGAFRTYPEG 200 (360)
Q Consensus 140 ~vVGWYHSHP~~g~~~S~iDI~tQ~~yQ~~~~-------p~V~LVvDp~~t~~~-G~v~ikAFRl~p~~ 200 (360)
++||||||||.++||||.+||++|+.||.+.+ |||+|||||..+... ....|+||++.|+.
T Consensus 80 ~vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~~~~s~i~~f~~~~~~ 148 (187)
T cd08067 80 SVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQITCFWVMPPP 148 (187)
T ss_pred EEEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCCCCCCcEEEEEEECCC
Confidence 99999999999999999999999999998764 899999999876432 34789999998854
No 7
>cd08062 MPN_RPN7_8 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in 19S proteasomal subunits Rpn7 and Rpn8. This family includes lid subunits of the 26 S proteasome regulatory particles, Rpn7 (PSMD7; proteasome 26S non-ATPase subunit 7; p44), and Rpn8 (PSMD8; proteasome 26S non-ATPase subunit 8; p40; Mov34). Rpn7 is known to be critical for the integrity of the 26 S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. Rpn7 and Rpn8 are ATP-independent components of the 19S regulator subunit, and contain the MPN structural motif on its N-terminal region. However, while they show a typical MPN metalloprotease fold, they lack the canonical JAMM motif, and therefore do not show catalytic isopeptidase activity. It is suggested that Rpn7 function is primarily structural.
Probab=99.96 E-value=7.1e-28 Score=232.29 Aligned_cols=201 Identities=21% Similarity=0.268 Sum_probs=161.0
Q ss_pred eEEEECHHHHHHHHHHHhc---CCCceeEEEeeeEecCCeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCC
Q 018129 61 KRVKISALALLKMVVHARS---GGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGR 137 (360)
Q Consensus 61 ~~V~Is~~vLlkIl~Ha~~---~~p~EV~GlLLG~~~~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~ 137 (360)
++|.|||+||++|++|+.+ +.+.+|+|+|||...++.++|+|||++|++.++++.+......+|+.+|+++++++++
T Consensus 1 ~~V~ihplVLl~I~dh~~R~~~~~~~~ViG~LLG~~~~~~veItnsF~~p~~~~~~~~~~~~~d~~y~~~m~~~~kkv~~ 80 (280)
T cd08062 1 KKVVVHPLVLLSVVDHYNRVAKGTSKRVVGVLLGSWKKGVLDVTNSFAVPFEEDEKDPSVWFLDHNYLENMYGMFKKVNA 80 (280)
T ss_pred CeEEEehHHHHHHHHHHhhhcCCCCceEEEEEEEEEeCCEEEEEEeeecCccCCCCCcchhhhhHHHHHHHHHHHHHhCC
Confidence 4799999999999999964 4478999999999999999999999999987766643222235899999999999999
Q ss_pred CCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCCCCCCCCCCCcccccchh
Q 018129 138 LENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEGYKPPDEPISEYQTIPLN 217 (360)
Q Consensus 138 ~e~vVGWYHSHP~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~t~~~G~v~ikAFRl~p~~~~~~~~~~~e~~~ip~~ 217 (360)
++.+||||||||+ ++..|+..|..|+++.+++|+|++||... .+++.++||...+.+...
T Consensus 81 ~e~vVGWY~tg~~----~~~~d~~ih~~~~~~~~~pv~l~vd~~~~--~~~lpi~aY~s~~~~~~~-------------- 140 (280)
T cd08062 81 KEKIVGWYSTGPK----LRPNDLDINELFRRYCPNPVLVIIDVRPK--DLGLPTEAYIAVEEVHDD-------------- 140 (280)
T ss_pred CCCeEEEecCCCC----CCcchHHHHHHHHHhCCCCEEEEEecCCC--CCCCceEEEEEeeeccCC--------------
Confidence 9999999999997 45567788888999999999999999763 567999999987754321
Q ss_pred hhhhhcC-ccceeEEeeEEEecChhHHHHHHHHhccccccccCCCCCccChHHHHHHHHHHHHHHHHHHHhh
Q 018129 218 KIEDFGV-HCKQYYSLDITYFKSSLDCHLLDLLWNKYWVNTLSSSPLLGNGDYVAGQISDLAEKLEQAENQL 288 (360)
Q Consensus 218 ki~d~g~-~~~~fyeLpV~i~~s~l~~~~L~~L~~~~w~~~Ls~s~ll~n~~~l~~~i~dl~~~~~~~~~~~ 288 (360)
|. .+..|.+||.++.....|+..++.|...- .+-+.+++...+....+.|..|..+++.+..=+
T Consensus 141 -----g~~~~~~F~~vp~~i~~~eaE~igve~l~r~~--~~~~~~~l~~~l~~~~~al~~L~~~l~~i~~Yl 205 (280)
T cd08062 141 -----GTPTSKTFVHVPSEIGAEEAEEVGVEHLLRDI--KDVTVSTLSTRVTNKLNSLKGLQSKLKEIKDYL 205 (280)
T ss_pred -----CCcceeEEEEcceEeeccchHHHHHHHHHhhc--cCcccchhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 11 35789999999999999999999997632 122334444577777788878877776665443
No 8
>cd08058 MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic. This family contains eukaryotic MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in proteins with a variety of functions, including AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase), BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as well as Rpn11 (regulatory particle number 11) and CSN5 (COP9 signalosome complex subunit 5). These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology. CSN5 is critical for nuclear export and the degradation of several tumor suppressor prot
Probab=99.96 E-value=1.2e-28 Score=208.74 Aligned_cols=113 Identities=39% Similarity=0.564 Sum_probs=96.5
Q ss_pred HHHHHHHHHhcCCCceeEEEeeeEec-----CCeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCCCCceEE
Q 018129 69 ALLKMVVHARSGGTIEVMGLMQGKTD-----GDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAVG 143 (360)
Q Consensus 69 vLlkIl~Ha~~~~p~EV~GlLLG~~~-----~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~~e~vVG 143 (360)
|+++|++||+++.|.|+||+|+|... ..+++|+++|+.|... ++.+ .|....+..++++++||
T Consensus 2 ~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~~---------~~~~---~~~~~~~~~~~g~~~vG 69 (119)
T cd08058 2 ALLKMLQHAESNTGIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSC---------TGEN---VEELFNVQTGRPLLVVG 69 (119)
T ss_pred HHHHHHHHhcCCCCeEEEEEeeeEEecCccceeEEEEeecCCCCCCc---------hhHH---HHHHHHHHhCCCCeEEE
Confidence 79999999999999999999999976 3458999999888632 1222 33444556789999999
Q ss_pred EEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEc
Q 018129 144 WYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTY 197 (360)
Q Consensus 144 WYHSHP~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~t~~~G~v~ikAFRl~ 197 (360)
||||||++++|||..||++|+.||.+.+++++||+||.++ ++++||||++
T Consensus 70 ~YHSHP~~~~~pS~~Di~~~~~~q~~~p~~~~lI~s~~~~----~~~~~a~rl~ 119 (119)
T cd08058 70 WYHSHPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKHR----NKDTGIFRLT 119 (119)
T ss_pred EEecCCCCCCccCHHHHHHHHHHhccCCCeEEEEECcCCC----CcccceEEeC
Confidence 9999999999999999999999999999999999999763 6799999984
No 9
>cd08068 MPN_BRCC36 Mov34/MPN/PAD-1 family: BRCC36, a subunit of BRCA1-A complex. BRCC36 (BRCA1-A complex subunit BRCC36; BRCA1/BRCA2-containing complex subunit 36; BRCA1/BRCA2-containing complex subunit 3; BRCC3; BRISC complex subunit BRCC36; BRCC36 isopeptidase complex; Lys-63-specific deubiquitinase BRCC36) and BRCC36-like domains are members of JAMM/MPN+ deubiquitinases (DUBs), possibly with Zn2+-dependent ubiquitin isopeptidase activity. BRCC36 is part of the BRCA1/BRCA2/BARD1-containing nuclear complex that displays an E3 ubiquitin ligase activity. It is targeted to DNA damage foci after irradiation; RAP80 recruits the Abraxas-BRCC36-BRCA1-BARD1 complex to DNA double strand breaks (DSBs) for DNA repair through specific recognition of Lys 63-linked polyubiquitinated proteins by its tandem ubiquitin-interacting motifs. A new protein, MERIT40 (mediator of RAP80 interactions and targeting 40 kDa), also named NBA1 (new component of the BRCA1 A complex), exists in the same BRCA1-contai
Probab=99.95 E-value=1.1e-27 Score=225.99 Aligned_cols=138 Identities=27% Similarity=0.455 Sum_probs=110.5
Q ss_pred eeEEEECHHHHHHHHHHHhcCCCceeEEEeeeEecC-------CeEEEEEEEeCCcc-cCCCccccccChHHH---HHHH
Q 018129 60 FKRVKISALALLKMVVHARSGGTIEVMGLMQGKTDG-------DAIIVMDAFALPVE-GTETRVNAQADAYEY---MVDY 128 (360)
Q Consensus 60 ~~~V~Is~~vLlkIl~Ha~~~~p~EV~GlLLG~~~~-------~~leVtd~F~lP~~-~te~~v~~~~e~~ey---~~~m 128 (360)
+++|+|++.++.+|+.||++++|.||||+|+|..++ ..+.|...++.++. ...+++++++ .++ +.++
T Consensus 1 l~~V~Is~~~l~~il~HA~~~~P~EvCGLL~G~~~~~~~~~~~~~v~i~~~~~~~~~~~s~~r~eidP--ee~~~a~~ea 78 (244)
T cd08068 1 LSKVHLSADVYLVCLTHALSTEKEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRSDKRKDRVEISP--EQLSAASTEA 78 (244)
T ss_pred CcEEEECHHHHHHHHHHHHhCCCcceeEEEEeecccccccccceeEEEeeeccccccCCCCceEEeCH--HHHHHHHHHH
Confidence 468999999999999999999999999999999853 33444444444442 3456776644 333 3445
Q ss_pred HHHHHHhCCCCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCC---CccCCeeeEEEEEEccC
Q 018129 129 SQTNKQAGRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTR---TVSAGKVEIGAFRTYPE 199 (360)
Q Consensus 129 l~~~r~v~~~e~vVGWYHSHP~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~---t~~~G~v~ikAFRl~p~ 199 (360)
-++.+..|+++.+||||||||+++||||.+|+++|..||++.+++++||+++.. +...|++.++|||+.+.
T Consensus 79 ~~~~~~~~rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v~lIvS~~~~~~~~~~~~~~i~aFr~~~g 152 (244)
T cd08068 79 ERLTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNEDKSTKMGEVQVTCFQSVQG 152 (244)
T ss_pred HHHHhhccCCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcEEEEEEecCCccccccCCEEEEEEEecCC
Confidence 556667899999999999999999999999999999999999999999998643 33468899999999874
No 10
>PF01398 JAB: JAB1/Mov34/MPN/PAD-1 ubiquitin protease; InterPro: IPR000555 Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This family is also known as the MPN domain [] and PAD-1-like domain []. It has been shown that this domain occurs in prokaryotes []. Mov34 proteins act as the regulatory subunit of the 26 proteasome, which is involved in the ATP-dependent degradation of ubiquitinated proteins. The function of this domain is unclear, but it is found in the N terminus of the proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. A number of the proteins associated with this family belong to MEROPS peptidase family M67 (clan M-). This includes the Poh1 peptidase of Saccharomyces cerevisiae (Baker's yeast) which is a component of the 19S proteasome regulatory particle.; GO: 0005515 protein binding; PDB: 2ZNV_D 2ZNR_A 4E0Q_A 2P87_A 2P8R_A 2O96_B 2O95_A 3RZU_F 3RZV_A.
Probab=99.94 E-value=3.9e-27 Score=197.15 Aligned_cols=112 Identities=30% Similarity=0.558 Sum_probs=97.4
Q ss_pred CeeEEEECHHHHHHHHHHHhcCCCceeEEEeeeEecCC-eEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCC
Q 018129 59 YFKRVKISALALLKMVVHARSGGTIEVMGLMQGKTDGD-AIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGR 137 (360)
Q Consensus 59 ~~~~V~Is~~vLlkIl~Ha~~~~p~EV~GlLLG~~~~~-~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~ 137 (360)
.+++|.|+++|+++|++||.+..+.||||+|+|..+++ +++|++||++|+.++++.+..... ++..+|+++++++++
T Consensus 2 s~~~V~i~p~vll~i~~h~~r~~~~~v~G~LlG~~~~~~~v~I~~~f~~p~~~~~~~~~~~~~--~~~~~~~~~~~~~~~ 79 (114)
T PF01398_consen 2 SVQTVQIHPLVLLKIIDHATRSSPNEVIGLLLGTQDGDNTVEITNSFPVPHSESEDDCDMDDE--DFQKKMIELLKKVNP 79 (114)
T ss_dssp SCEEEEEEHHHHHHHHHHHHHHHCTEEEEEEEEEEETT-EEEEEEEEEESEEEESSEEEEECC--HHHHHHHHHHHHCST
T ss_pred CcEEEEECHHHHHHHHHHHhcCCCCEEEEEEEEEecCceEEEEEEEEEeeEecCccccccchh--hHHHHHHhhhccccc
Confidence 57899999999999999998877889999999999999 999999999999887776555433 344789999999989
Q ss_pred CCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCC
Q 018129 138 LENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEP 172 (360)
Q Consensus 138 ~e~vVGWYHSHP~~g~~~S~iDI~tQ~~yQ~~~~p 172 (360)
++.+||||||||.++||||..||++|..||++.++
T Consensus 80 ~~~iVGWY~s~p~~~~~~S~~di~~q~~~q~~~~~ 114 (114)
T PF01398_consen 80 NLEIVGWYHSHPNISCFPSPTDIETQKQYQRMNPN 114 (114)
T ss_dssp TSEEEEEEEEESSS-SS--HHHHHHHHHHHHHTTT
T ss_pred cceEEEEEEccCCccccCCHHHHHHHHHHHHhCCC
Confidence 99999999999999999999999999999998763
No 11
>smart00232 JAB_MPN JAB/MPN domain. Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.
Probab=99.94 E-value=3.8e-26 Score=194.21 Aligned_cols=134 Identities=31% Similarity=0.480 Sum_probs=119.8
Q ss_pred EEEECHHHHHHHHHHHhcCCCceeEEEeeeEecCCeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCCCCce
Q 018129 62 RVKISALALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENA 141 (360)
Q Consensus 62 ~V~Is~~vLlkIl~Ha~~~~p~EV~GlLLG~~~~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~~e~v 141 (360)
.|+|++.++++|++|+.+..|.|+||+|+|+..+++++|+++|++|+....+++.. ...+|+..|.+..++.++++.+
T Consensus 1 ~v~i~~~v~~~i~~h~~~~~p~e~~G~L~G~~~~~~~~i~~~~~~p~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~ 78 (135)
T smart00232 1 EVKVHPLVPLNILKHAIRDGPEEVCGVLLGKSNKDRPEVKEVFAVPNEPQDDSVQE--YDEDYSHLMDEELKKVNKDLEI 78 (135)
T ss_pred CEEEcHHHHHHHHHHHhcCCCcEEEEEEEEEEcCCEEEEEEEEecCcCCCCcchhh--hhhhHHHHHHHHHHhhCCCceE
Confidence 37899999999999999999999999999999999999999999998765554321 2346788888888999999999
Q ss_pred EEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEcc
Q 018129 142 VGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYP 198 (360)
Q Consensus 142 VGWYHSHP~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~t~~~G~v~ikAFRl~p 198 (360)
||||||||..+++||..|+.+|..+|.....++++++||.++. .|++.++||++.+
T Consensus 79 vGwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~s~-~g~~~~~af~~~~ 134 (135)
T smart00232 79 VGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKSF-QGRLSLRAFRLTP 134 (135)
T ss_pred EEEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCccc-cCcEEEEEEEecC
Confidence 9999999999999999999999999999999999999999975 5999999999865
No 12
>cd08057 MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity (non metal-binding); eukaryotic. This family contains MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains variants lacking key residues in the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Rpn7/PSMD7, Rpn8/PSMD8, CSN6, Prp8p, and the translation initiation factor 3 subunits f and h do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function. Rpn7 is known to be critical for the integrity of the 26S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. CSN6 is a highly conserved protein complex with diverse functions, including several import
Probab=99.94 E-value=1.9e-26 Score=204.31 Aligned_cols=134 Identities=27% Similarity=0.397 Sum_probs=113.2
Q ss_pred EEECHHHHHHHHHHHhcCC--CceeEEEeeeEecCCeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCCCCc
Q 018129 63 VKISALALLKMVVHARSGG--TIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLEN 140 (360)
Q Consensus 63 V~Is~~vLlkIl~Ha~~~~--p~EV~GlLLG~~~~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~~e~ 140 (360)
|+|||+|+++|++|+.+.. +.+|+|+|||...+++++|+|||++|.+.+++.... ..+|+.+|+++++++++++.
T Consensus 1 V~ihplvll~I~dh~~R~~~~~~~v~G~LlG~~~~~~veV~nsF~lp~~~~~~~~~~---d~~y~~~m~~~~~~v~~~~~ 77 (157)
T cd08057 1 VQLHPLVLLNISDHYTRRKYGIKRVIGVLLGYVDGDKIEVTNSFELPFDEEEESIFI---DTEYLEKRYNLHKKVYPQEK 77 (157)
T ss_pred CEEccHHHhhHHHHHHhccCCCCeEEEEEEeEEeCCEEEEEEeEEccccCCCcchhh---hHHHHHHHHHHHHHhCCCCC
Confidence 6899999999999997665 899999999999999999999999999776655332 35899999999999999999
Q ss_pred eEEEEecCCCCCCccCHHhHHHHHhhhhc-CCCeEEEEEcCCCCccCCeeeEEEEEEccC
Q 018129 141 AVGWYHSHPGYGCWLSGIDVSTQMLNQQF-QEPFLAVVIDPTRTVSAGKVEIGAFRTYPE 199 (360)
Q Consensus 141 vVGWYHSHP~~g~~~S~iDI~tQ~~yQ~~-~~p~V~LVvDp~~t~~~G~v~ikAFRl~p~ 199 (360)
+|||||+|+..+++++..|...+..|... .+++|+|++||.++...|++.|+|||+.+.
T Consensus 78 vVGWY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~~~~~~l~i~ay~~~~~ 137 (157)
T cd08057 78 IVGWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQSDSEKLEISTFTSAQR 137 (157)
T ss_pred EEEEEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcccCCCcccEEEEEEecC
Confidence 99999999987766766666555555443 678899999998744478899999999863
No 13
>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=4.8e-26 Score=219.65 Aligned_cols=192 Identities=38% Similarity=0.575 Sum_probs=152.9
Q ss_pred eeEEEECHHHHHHHHHHHhcCCCce-eEEEe-ee---E-ecCCeEEEEEEEeCCcccCCCc--cccccChHHHHHHHHHH
Q 018129 60 FKRVKISALALLKMVVHARSGGTIE-VMGLM-QG---K-TDGDAIIVMDAFALPVEGTETR--VNAQADAYEYMVDYSQT 131 (360)
Q Consensus 60 ~~~V~Is~~vLlkIl~Ha~~~~p~E-V~GlL-LG---~-~~~~~leVtd~F~lP~~~te~~--v~~~~e~~ey~~~ml~~ 131 (360)
-++|.|+.+++++|++|.|.+.|.| +||+| +| . ++..++.|.+.|+.|..++.-. +++. + .-|+.+|+++
T Consensus 30 ~e~v~i~slall~m~rh~r~~~p~e~v~Glm~lg~~~~fv~~~Tv~vv~v~am~~sg~~is~~~e~~-d-~V~q~q~~~~ 107 (316)
T KOG1555|consen 30 KETVYISSLALLKMLRHDRAGSPEETVMGLMSLGRLPEFVDDYTVRVVDVFAMPQSGTGISKFVEAV-D-PVFQTQMMDL 107 (316)
T ss_pred cceeeeehhhhhhcccccccCCchhhccceeecccccceeeecceeeeeeeccccccceecccchhc-c-HHHHHHHHHH
Confidence 4579999999999999999999999 99999 99 3 3567889999999999886644 3322 2 2578999999
Q ss_pred HHHhCCCCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCC-CCCCCCCCCc
Q 018129 132 NKQAGRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEG-YKPPDEPISE 210 (360)
Q Consensus 132 ~r~v~~~e~vVGWYHSHP~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~t~~~G~v~ikAFRl~p~~-~~~~~~~~~e 210 (360)
++..|+.+.|||||||||+++||||..||+||..||...+..++.++||..+. .|++.+.|||+.... ..++.+++..
T Consensus 108 l~~tGrp~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~S~-~g~vv~d~f~~In~~~~~~~~eprqt 186 (316)
T KOG1555|consen 108 LKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQSP-YGKVVPDAFSSINPQWISPGGEPRQT 186 (316)
T ss_pred HHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeecccCC-CCCccCChhhhcCcccccCCCCCccc
Confidence 99999999999999999999999999999999999999999999999999886 899999999996432 2222111110
Q ss_pred cc-ccchhh----hh-hhcCccceeEEeeEEEecChhHHHHHHHHhcccccc
Q 018129 211 YQ-TIPLNK----IE-DFGVHCKQYYSLDITYFKSSLDCHLLDLLWNKYWVN 256 (360)
Q Consensus 211 ~~-~ip~~k----i~-d~g~~~~~fyeLpV~i~~s~l~~~~L~~L~~~~w~~ 256 (360)
+. ..+.++ .+ -+|. +.||.++|.++..++++.++..+..+.|..
T Consensus 187 ts~~~~m~~~~s~q~~~~g~--n~y~~~ei~~~v~~~~~~~~~nv~~~s~~~ 236 (316)
T KOG1555|consen 187 TSNGGHMDMQESLQEDIHGL--NRYYRIEIPLHVLPYEQLMLLNVPLKSWKS 236 (316)
T ss_pred cccccccccchhHHhHhhcc--CceEEEEeeEEechhhhhchhccchhhhhh
Confidence 00 012222 22 2443 379999999999999999999998777765
No 14
>KOG2975 consensus Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=1.4e-25 Score=210.00 Aligned_cols=195 Identities=20% Similarity=0.257 Sum_probs=160.3
Q ss_pred eEEEECHHHHHHHHHHHh--cCCCceeEEEeeeEecCCeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCCC
Q 018129 61 KRVKISALALLKMVVHAR--SGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRL 138 (360)
Q Consensus 61 ~~V~Is~~vLlkIl~Ha~--~~~p~EV~GlLLG~~~~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~~ 138 (360)
-+|+|+|.|++.|++|.. ..+..+|||+|||..+++.++|||||++|+.+.+++++.++ +|..+|++++++++++
T Consensus 21 ltv~ihP~Vlf~ivD~~~RR~~~~~rviGTLLG~~~~g~ieitNCFaVPhnEssdqvevdm---~y~~~M~~l~~k~npn 97 (288)
T KOG2975|consen 21 LTVRLHPVVLFSIVDAYERRNKGAERVIGTLLGTVDKGSVEVTNCFAVPHNESSDQVEVDM---EYAKNMYELHKKVNPN 97 (288)
T ss_pred ceEEEcceEEeEeehhhhcCCccchhhhhheeecccCCeEEEEEeeeccCccccccceeeH---HHHHHHHHHhcccCCC
Confidence 479999999999999984 46789999999999999999999999999999999998866 7999999999999999
Q ss_pred CceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCCCCCCCCCCCcccccchhh
Q 018129 139 ENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEGYKPPDEPISEYQTIPLNK 218 (360)
Q Consensus 139 e~vVGWYHSHP~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~t~~~G~v~ikAFRl~p~~~~~~~~~~~e~~~ip~~k 218 (360)
|.+||||.|.++...+.|.| |..|-+..+++|+|.||+..+ +|++.||||..++.|. |-..
T Consensus 98 E~vvGWyaTg~dvt~~ssli----hdyYare~~~pvhLtVDT~~~--n~rm~ikaYvss~~Gv-------------pg~~ 158 (288)
T KOG2975|consen 98 ELVVGWYATGHDVTEHSSLI----HDYYAREAPNPVHLTVDTSLQ--NGRMSIKAYVSSLMGV-------------PGRT 158 (288)
T ss_pred ceeEEEEecCCCcccchhHH----HHHhhccCCCCeEEEEecccc--CCccceeEEEEeccCC-------------CCcc
Confidence 99999999999998887765 567878889999999998764 7999999999987663 3211
Q ss_pred hhhhcCccceeEEeeEEEecChhHHHHHHHHhccc-cccccCCCCCccChHHHHHHHHHHHHHHHHHH
Q 018129 219 IEDFGVHCKQYYSLDITYFKSSLDCHLLDLLWNKY-WVNTLSSSPLLGNGDYVAGQISDLAEKLEQAE 285 (360)
Q Consensus 219 i~d~g~~~~~fyeLpV~i~~s~l~~~~L~~L~~~~-w~~~Ls~s~ll~n~~~l~~~i~dl~~~~~~~~ 285 (360)
. ..+|.+|||++...+.++..|+.+.... ... ...+++..++.+.....+|...++++.
T Consensus 159 ---~---~~mF~plpvel~~~~~ervgl~li~kt~~sp~--r~~~l~~dLqQv~~at~~l~~~L~~Vl 218 (288)
T KOG2975|consen 159 ---M---GVMFTPLPVELAYYDAERVGLDLIEKTSFSPS--RVAGLSSDLQQVEGATARLQSLLERVL 218 (288)
T ss_pred ---c---ceeeeeeeeEEeecchhhhHHHHHHHhccChh--hhccccchHHHHHHHHHHHHHHHHHHH
Confidence 1 2499999999999999999999997553 222 234566677766666655555555443
No 15
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=99.93 E-value=1.3e-24 Score=211.61 Aligned_cols=203 Identities=18% Similarity=0.202 Sum_probs=156.1
Q ss_pred CCCCeeEEEECHHHHHHHHHHHhcCC---CceeEEEeeeEecCCeEEEEEEEeCCcccCCCc---cccccChHHHHHHHH
Q 018129 56 DPHYFKRVKISALALLKMVVHARSGG---TIEVMGLMQGKTDGDAIIVMDAFALPVEGTETR---VNAQADAYEYMVDYS 129 (360)
Q Consensus 56 ~p~~~~~V~Is~~vLlkIl~Ha~~~~---p~EV~GlLLG~~~~~~leVtd~F~lP~~~te~~---v~~~~e~~ey~~~ml 129 (360)
.|.++.+|.|||+|+++|++||.+.. +.+|+|.|||...++.++|+|||++|+...++. +..+ .+|+.+|+
T Consensus 1 ~~~~~~~V~vhPlVll~I~dh~~R~~~~~~~rviG~LLG~~~~~~ieItnsF~~p~~e~~~~~~~~~~D---~~y~~~m~ 77 (303)
T PLN03246 1 SPRGIEKVVVHPLVLLSIVDHYNRVAKDTRKRVVGVLLGSSFRGRVDVTNSFAVPFEEDDKDPSIWFLD---HNYLESMF 77 (303)
T ss_pred CCCCCcEEEECcHHHHHHHHHHHhccCCCCCeeEEEEEeeecCCEEEEEeccccCcccCCCCccceeec---HHHHHHHH
Confidence 37889999999999999999996543 567999999999999999999999998654332 2222 48999999
Q ss_pred HHHHHhCCCCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCCCCCCCCCCC
Q 018129 130 QTNKQAGRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEGYKPPDEPIS 209 (360)
Q Consensus 130 ~~~r~v~~~e~vVGWYHSHP~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~t~~~G~v~ikAFRl~p~~~~~~~~~~~ 209 (360)
++++++++++.+||||+|.|... ..|+..|..|.++.+.+|+|++|+... .+++.++||...+.+....
T Consensus 78 ~~~k~V~~~~~vVGWY~tg~~i~----~~d~~IH~~~~~~~~~Pv~L~vD~~~~--~~~lpi~aY~s~~~~~~~~----- 146 (303)
T PLN03246 78 GMFKRINAKEHVVGWYSTGPKLR----ENDLDIHELFNDYVPNPVLVIIDVQPK--ELGIPTKAYYAVEEVKENA----- 146 (303)
T ss_pred HHHHHhCCCCcEEeeecCCCCCC----cchHHHHHHHHhhCCCCeEEEEecCCC--CCCCceEEEEEEEeccCCC-----
Confidence 99999999999999999999744 345666677888888899999998653 5679999999876543110
Q ss_pred cccccchhhhhhhcCccceeEEeeEEEecChhHHHHHHHHhccccccccCCCCCccChHHHHHHHHHHHHHHHHHHH
Q 018129 210 EYQTIPLNKIEDFGVHCKQYYSLDITYFKSSLDCHLLDLLWNKYWVNTLSSSPLLGNGDYVAGQISDLAEKLEQAEN 286 (360)
Q Consensus 210 e~~~ip~~ki~d~g~~~~~fyeLpV~i~~s~l~~~~L~~L~~~~w~~~Ls~s~ll~n~~~l~~~i~dl~~~~~~~~~ 286 (360)
-+..+..|.+||.++.....|+..++.|...-- +=+.+.+...+......|..|.++++.+..
T Consensus 147 ------------~~~~~~~F~~vp~~i~~~EaE~Igve~l~r~~~--~~~~s~l~~~l~~~~~al~~L~~rl~~i~~ 209 (303)
T PLN03246 147 ------------TQKSQKVFVHVPSEIGAHEAEEIGVEHLLRDVK--DTTVSTLATEVTGKLTALKGLDARLREIRS 209 (303)
T ss_pred ------------CcccccEEEECCeeeeecCHHHHHHHHHHhccc--CCccchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 011347899999999999999999999985422 112233334666667777777766665543
No 16
>cd08063 MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6. CSN6 (COP9 signalosome subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one of the eight subunits of COP9 signalosome, a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, developmental changes, and some aspects of immune responses. CSN6 is an MPN-domain protein that directly interacts with the MPN+-domain subunit CSN5. It is cleaved during apoptosis by activated caspases. CSN6 processing occurs in CSN/CRL (cullin-RING Ub ligase) complexes and is followed by the cleavage of Rbx1, the direct interaction partner of CSN6. CSN6 cleavage enhances CSN-mediated deneddylating activity (i.e. cleavage of ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells. The cleav
Probab=99.92 E-value=8.7e-24 Score=204.63 Aligned_cols=201 Identities=19% Similarity=0.240 Sum_probs=154.1
Q ss_pred EEEECHHHHHHHHHHHhc----CC--CceeEEEeeeEecCCeEEEEEEEeCCcccCC-CccccccChHHHHHHHHHHHHH
Q 018129 62 RVKISALALLKMVVHARS----GG--TIEVMGLMQGKTDGDAIIVMDAFALPVEGTE-TRVNAQADAYEYMVDYSQTNKQ 134 (360)
Q Consensus 62 ~V~Is~~vLlkIl~Ha~~----~~--p~EV~GlLLG~~~~~~leVtd~F~lP~~~te-~~v~~~~e~~ey~~~ml~~~r~ 134 (360)
+|.|||+||++|++|+.+ .. +..|+|.|||..+++.++|+|||++|+..++ .....+ .+|+.+|++++++
T Consensus 2 ~V~lHPlVll~I~dH~~R~~~~~~~~~~~v~G~LLG~~~~~~veItnsF~~p~~~~~~~~~~id---~~y~~~m~~~~kk 78 (288)
T cd08063 2 SVKLHPLVILNISDHITRHRAQSQSEPPRVVGALLGQQDGREIEIENSFELKYDTNEDGEIVLD---KEFLETRLEQFKQ 78 (288)
T ss_pred eEEEecceeeeHHhhHhHHhccCCCCCCcEEEEEEEEEcCCEEEEEEEEecccccCCCCceeeC---HHHHHHHHHHHHH
Confidence 689999999999999965 23 6899999999999999999999999997655 333332 4899999999999
Q ss_pred hCCCCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCCCCCCCCCCCccccc
Q 018129 135 AGRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEGYKPPDEPISEYQTI 214 (360)
Q Consensus 135 v~~~e~vVGWYHSHP~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~t~~~G~v~ikAFRl~p~~~~~~~~~~~e~~~i 214 (360)
+++++.+||||+|++. +...+...|+.| |....+++|+|++||..+...|++.++||+..+.+-..
T Consensus 79 V~~~~~vVGWY~tg~~-~~~~~~~~Ih~~--~~~~~~~pv~L~~D~~~~~~~~~lpi~ay~s~~~~~~~----------- 144 (288)
T cd08063 79 VFKDLDFVGWYTTGPG-GPTESDLPIHKQ--ILEINESPVLLLLDPEANASGKDLPVTIYESVLELVDG----------- 144 (288)
T ss_pred hccCCceEEEEecCCC-CCCHHHHHHHHH--HHhhCCCcEEEEEccccccCCCCCceeEEEEEEeccCC-----------
Confidence 9999999999999996 666665555554 44566778999999987423678999999987654210
Q ss_pred chhhhhhhcCccceeEEeeEEEecChhHHHHHHHHhccccccccCCCCCccChHHHHHHHHHHHHHHHHHHHhh
Q 018129 215 PLNKIEDFGVHCKQYYSLDITYFKSSLDCHLLDLLWNKYWVNTLSSSPLLGNGDYVAGQISDLAEKLEQAENQL 288 (360)
Q Consensus 215 p~~ki~d~g~~~~~fyeLpV~i~~s~l~~~~L~~L~~~~w~~~Ls~s~ll~n~~~l~~~i~dl~~~~~~~~~~~ 288 (360)
.....|.++|.++..+..|+..++.|....-..+=+.+.+...+..+...+..|..+++....-+
T Consensus 145 ---------~~~~~F~~i~~~i~~~eaErIgv~~l~~~~~~~~~~~~~~~~~l~~~~~al~~L~~rl~~i~~Yl 209 (288)
T cd08063 145 ---------EATLRFRELPYTIETGEAERIGVDHVARGGASGSSEKSTVAAHLQAQHNAIKMLNSRVELILEYL 209 (288)
T ss_pred ---------ccccEEEeeeeEEEeccCceeeHHHHHhcCCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 12468999999999999999999999865422222233344667777777777776665554433
No 17
>cd08066 MPN_AMSH_like Mov34/MPN/PAD-1 family. AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM (signal-transducing adapter molecule, also known as STAMBP)) and AMSH-like proteins (AMSH-LP) are members of JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent ubiquitin isopeptidase activity. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. AMSH and AMSH-LP are anchored on the early endosomal membrane via interaction with the clathrin coat. AMSH shares a common SH3-binding site with another endosomal DUB, UBPY (ubiquitin-specific protease Y; also known as USP8), the latter being a cysteine protease that does not discriminate between Lys48 and Lys63-linked ubiquitin. AMSH is involved in the degradation of EGF receptor (EGFR) and possibly other ubiquitinated endocytosed proteins. AMSH also interacts with CHMP1, CHMP2, and CHMP3 proteins, al
Probab=99.92 E-value=8.8e-24 Score=190.79 Aligned_cols=131 Identities=24% Similarity=0.396 Sum_probs=111.2
Q ss_pred eeEEEECHHHHHHHHHHHhcC--CCceeEEEeeeEecCCeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCC
Q 018129 60 FKRVKISALALLKMVVHARSG--GTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGR 137 (360)
Q Consensus 60 ~~~V~Is~~vLlkIl~Ha~~~--~p~EV~GlLLG~~~~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~ 137 (360)
++.+.|+..++.+|+.||+.. .|.|+||+|+|...++..+|++++..|+.+++..+++.. ..+ +++.++ .+
T Consensus 1 ~~~l~Ipk~il~~~l~~A~~~~~~p~E~cGlL~G~~~~~~~~I~~i~~~~q~~~~~~~~~~~-~~e----~~~~~~--~~ 73 (173)
T cd08066 1 LRQVVVPADLMDKFLQLAEPNTSRNLETCGILCGKLSNNAFFITHLIIPKQSGTSDSCQTTN-EEE----LFDFQD--QH 73 (173)
T ss_pred CeEEEECHHHHHHHHHHHHhCCCCCCeEEEEEEeEcCCCeEEEEEEEeccccCCCceecCCC-HHH----HHHHHH--hC
Confidence 357899999999999999987 469999999999888888999998889888877766533 222 444444 35
Q ss_pred CCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEc-cCCCCC
Q 018129 138 LENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTY-PEGYKP 203 (360)
Q Consensus 138 ~e~vVGWYHSHP~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~t~~~G~v~ikAFRl~-p~~~~~ 203 (360)
++.+||||||||+.+||||..|+++|..||.+.+++++|||+|. .++++|||+. |+|+.-
T Consensus 74 gle~vGwyHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvSp~------~~~l~afrl~~~~g~~~ 134 (173)
T cd08066 74 DLITLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAPK------YNEFGIFRLTDPPGLDE 134 (173)
T ss_pred CCeeEEEEeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEECCC------CcEEeEEEeecCCccee
Confidence 79999999999999999999999999999999999999999983 5699999999 777653
No 18
>cd07767 MPN Mpr1p, Pad1p N-terminal (MPN) domains. MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors. These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. J
Probab=99.88 E-value=2.6e-22 Score=166.88 Aligned_cols=115 Identities=23% Similarity=0.340 Sum_probs=93.9
Q ss_pred HHHHHHHhcCCCceeEEEeeeEecCCeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCCCCceEEEEecCCC
Q 018129 71 LKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAVGWYHSHPG 150 (360)
Q Consensus 71 lkIl~Ha~~~~p~EV~GlLLG~~~~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~~e~vVGWYHSHP~ 150 (360)
.+|++||+...|.||||+|+|+..+++++|+++|++|+..++... +..++ |....+..+.++.+||||||||.
T Consensus 2 k~il~~a~~~~~~ev~G~L~G~~~~~~~~i~~~~~~~~~~~~~~~----~~~~~---~~~~~~~~~~~~~iVGwyhshp~ 74 (116)
T cd07767 2 KMFLDAAKSINGKEVIGLLYGSKTKKVLDVDEVIAVPFDEGDKDD----NVWFL---MYLDFKKLNAGLRIVGWYHTHPK 74 (116)
T ss_pred HhHHHHHhcCCCcEEEEEeEEEEcCCEEEEEEEEecccCCCCCcc----HHHHH---HHHHHHHhcCCCeEEEEEEcCCC
Confidence 579999999899999999999999889999999999986543321 11122 34445566789999999999999
Q ss_pred CCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEE
Q 018129 151 YGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAF 194 (360)
Q Consensus 151 ~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~t~~~G~v~ikAF 194 (360)
.+++||..|+.+|..||+..+++++||+|+... ...+.++||
T Consensus 75 ~~~~~s~~dv~~~~~~q~~~~~~v~li~~~~~~--~~~~~~~~~ 116 (116)
T cd07767 75 PSCFLSPNDLATHELFQRYFPEKVMIIVDVKPK--DLGNSWKCY 116 (116)
T ss_pred CCCccCHHHHHHHHHHHHhCCCCEEEEEECCCc--cCCCCcccC
Confidence 999999999999999999889999999999763 224667765
No 19
>cd08070 MPN_like Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding). This family contains archaeal and bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=99.79 E-value=2.4e-18 Score=147.35 Aligned_cols=119 Identities=24% Similarity=0.285 Sum_probs=95.0
Q ss_pred HHHHHHHHHHhcCCCceeEEEeeeEecCCeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCCCCceEEEEec
Q 018129 68 LALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAVGWYHS 147 (360)
Q Consensus 68 ~vLlkIl~Ha~~~~p~EV~GlLLG~~~~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~~e~vVGWYHS 147 (360)
.++.+|+.||+++.|.|+||+|+|..++....|+.++++|+...+.+..+..++.+ +.++.+.+++ .++.+||||||
T Consensus 2 ~~~~~il~ha~~~~P~E~cGlL~G~~~~~~~~i~~~~p~~n~~~~~~~~f~~d~~~-~~~~~~~~~~--~g~~~vG~~HS 78 (128)
T cd08070 2 ELLEAILAHAEAEYPEECCGLLLGKGGGVTAIVTEVYPVRNVAESPRRRFEIDPAE-QLAAQREARE--RGLEVVGIYHS 78 (128)
T ss_pred HHHHHHHHHHHhCCCCceEEEEEeecCCCCceEEEEEEccCCCCCCCceEEECHHH-HHHHHHHHHH--CCCeEEEEEeC
Confidence 36789999999999999999999999887778899999999766543444456655 4455666664 35999999999
Q ss_pred CCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEcc
Q 018129 148 HPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYP 198 (360)
Q Consensus 148 HP~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~t~~~G~v~ikAFRl~p 198 (360)
||+.+++||..|+..+. ..+.++||+++.. +...++||++..
T Consensus 79 HP~~~~~PS~~D~~~~~-----~~~~~~lIv~~~~----~~~~~~~~~~~~ 120 (128)
T cd08070 79 HPDGPARPSETDLRLAW-----PPGVSYLIVSLAG----GAPELRAWRLEG 120 (128)
T ss_pred CCCCCCCCCHHHHHhcc-----CCCCeEEEEECCC----CCcEEEEEEEcC
Confidence 99999999999998642 3478999999743 356899999854
No 20
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=99.76 E-value=7.9e-18 Score=156.84 Aligned_cols=166 Identities=22% Similarity=0.330 Sum_probs=127.1
Q ss_pred CCeeEEEECHHHHHHHHHHHhcC---CCceeEEEeeeEecCCeEEEEEEEeCCcccCCCc--cccccChHHHHHHHHHHH
Q 018129 58 HYFKRVKISALALLKMVVHARSG---GTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETR--VNAQADAYEYMVDYSQTN 132 (360)
Q Consensus 58 ~~~~~V~Is~~vLlkIl~Ha~~~---~p~EV~GlLLG~~~~~~leVtd~F~lP~~~te~~--v~~~~e~~ey~~~ml~~~ 132 (360)
..+.+|.|+|+||+..++|..+. ...+|.|+|||...++++.|+|+|++|.++.+.. +.+- ...|+..|..++
T Consensus 6 ~~~~kViVhPLVLLS~VDhynR~~k~~~KRvvGvLLG~~~~~~i~vtnSfAvpFeEDdk~~svWFl--Dh~Y~esM~~mf 83 (309)
T KOG1556|consen 6 LTVEKVIVHPLVLLSAVDHYNRVGKDTNKRVVGVLLGSWNGDVIDVTNSFAVPFEEDDKDKSVWFL--DHNYIESMFGMF 83 (309)
T ss_pred cccceeeeehhHHHHHHHHHhhhccCcCceEEEEEEecCCCCeEEeecceeccccccCCCCceEEe--ccHHHHHHHHHH
Confidence 45789999999999999999753 3489999999999999999999999999876543 2331 237999999999
Q ss_pred HHhCCCCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCe--eeEEEEEEccCCCCCCCCCCCc
Q 018129 133 KQAGRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGK--VEIGAFRTYPEGYKPPDEPISE 210 (360)
Q Consensus 133 r~v~~~e~vVGWYHSHP~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~t~~~G~--v~ikAFRl~p~~~~~~~~~~~e 210 (360)
++++..+.+||||||+|.. ..+.+||. ...-++.|+.|.+|||... +. +...||-..
T Consensus 84 kKvNakekivGWYhTGPkl--~~nDl~In--~l~k~y~pnpvLvIIdvkp----k~~gLPT~AY~aV------------- 142 (309)
T KOG1556|consen 84 KKVNAKEKVVGWYHTGPKL--RENDLDIN--ELLKRYVPNPVLVIIDVKP----KELGLPTEAYIAV------------- 142 (309)
T ss_pred HHhcchhheeeeeccCCcc--ccchhhHH--HHHhhcCCCceEEEEeccc----ccCCCCchheeee-------------
Confidence 9999999999999999964 34555554 4556788899999999642 22 233455332
Q ss_pred ccccchhhhhhhcC-ccceeEEeeEEEecChhHHHHHHHHhcc
Q 018129 211 YQTIPLNKIEDFGV-HCKQYYSLDITYFKSSLDCHLLDLLWNK 252 (360)
Q Consensus 211 ~~~ip~~ki~d~g~-~~~~fyeLpV~i~~s~l~~~~L~~L~~~ 252 (360)
+-+++-|+ ...-|.-+|.+|---..+....+-|-.+
T Consensus 143 ------eev~dDgt~t~ktF~Hvps~I~AeEAEEvGVEHLlRD 179 (309)
T KOG1556|consen 143 ------EEVKDDGTPTSKTFVHVPSEIEAEEAEEVGVEHLLRD 179 (309)
T ss_pred ------eeeecCCCCccceeEecCcccchhHHHHhhHHHHHHH
Confidence 23344443 3467999999999888988888888544
No 21
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=99.57 E-value=1.9e-14 Score=124.36 Aligned_cols=104 Identities=28% Similarity=0.334 Sum_probs=72.9
Q ss_pred EEECHHHHHHHHHHHhcCCCceeEEEeeeEecCCeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCCCCceE
Q 018129 63 VKISALALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAV 142 (360)
Q Consensus 63 V~Is~~vLlkIl~Ha~~~~p~EV~GlLLG~~~~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~~e~vV 142 (360)
+.|...++-.|+.|++++.|.|+||+|+|...+ ...|.+++...+....... ..++.. +...++ ..++.+|
T Consensus 2 ~~i~~~~l~~il~~a~~~~p~E~~g~l~~~~~~-----~~~~~~~n~~~~~~~~~~~-~~~~~~-~~~~~~--~~g~~vv 72 (134)
T COG1310 2 LVIPKEVLGAILEHARREHPREVCGLLAGTREG-----ERYFPLKNVSVEPVEYFEI-DPEYSL-FYLAAE--DAGEVVV 72 (134)
T ss_pred ceecHHHHHHHHHHHHhcCChheEEEEEeeccc-----ceeeccccccCCcceeEee-CHHHHH-HHHHHh--hCCCEEE
Confidence 568899999999999999999999999999876 5566666654432111111 123333 344444 3459999
Q ss_pred EEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEc
Q 018129 143 GWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVID 179 (360)
Q Consensus 143 GWYHSHP~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvD 179 (360)
|||||||+.+||||..|+. .|.+.+...+||+.
T Consensus 73 g~yHSHP~~~~~pS~~D~~----~~~~~~~~~~iv~~ 105 (134)
T COG1310 73 GWYHSHPGGPPYPSEADRR----LSKLGPLPWLIVSV 105 (134)
T ss_pred EEEcCCCCCCCCcCHHHHh----hccccCCCEEEEEc
Confidence 9999999999999999997 34444443344444
No 22
>cd08072 MPN_archaeal Mov34/MPN/PAD-1 family: archaeal JAB1/MPN/Mov34 metalloenzyme. This family contains only archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=99.54 E-value=8.4e-14 Score=118.23 Aligned_cols=108 Identities=20% Similarity=0.184 Sum_probs=80.8
Q ss_pred ECHHHHHHHHHHHhcCCCceeEEEeeeEecCCeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCCCCceEEE
Q 018129 65 ISALALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAVGW 144 (360)
Q Consensus 65 Is~~vLlkIl~Ha~~~~p~EV~GlLLG~~~~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~~e~vVGW 144 (360)
|...++-.|+.||+++.|.|+||+|+|+.. .|++++++|+....+.. . .|-.+ ++ ..+..+||.
T Consensus 1 i~~~~~~~i~~ha~~~~P~E~CGlL~G~~~----~v~~~~~~~n~~~~~~~-~-----~f~~~----~~--~~g~~ivgi 64 (117)
T cd08072 1 ISRDLLDSILEAAKSSHPNEFAALLRGKDG----VITELLILPGTESGEVS-A-----VFPLL----ML--PLDMSIVGS 64 (117)
T ss_pred CCHHHHHHHHHHHhhcCCceEEEEEEeecc----EEEEEEECCCCCCCCcc-e-----eechH----Hh--cCCCeEEEE
Confidence 456788999999999999999999999764 68999999976433221 1 11112 12 246899999
Q ss_pred EecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEc
Q 018129 145 YHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTY 197 (360)
Q Consensus 145 YHSHP~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~t~~~G~v~ikAFRl~ 197 (360)
|||||+.+++||..|+... ..++.++||+++-. ..-.++||+..
T Consensus 65 ~HSHP~~~~~PS~~D~~~~-----~~~~~~~lIvs~~~----~~~~~~a~~~~ 108 (117)
T cd08072 65 VHSHPSGSPRPSDADLSFF-----SKTGLVHIIVGYPY----DEDDWRAYDSD 108 (117)
T ss_pred EEcCCCCCCCCCHHHHHhh-----hcCCCEEEEEECcC----CCCCEEEEecC
Confidence 9999999999999998632 34788999999532 12368999874
No 23
>KOG2880 consensus SMAD6 interacting protein AMSH, contains JAB/MPN/Mov34 domain [Signal transduction mechanisms]
Probab=99.50 E-value=2e-14 Score=140.05 Aligned_cols=131 Identities=21% Similarity=0.371 Sum_probs=107.6
Q ss_pred CCCCeeEEEECHHHHHHHHHHHhcC--CCceeEEEeeeEecCCeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHH
Q 018129 56 DPHYFKRVKISALALLKMVVHARSG--GTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNK 133 (360)
Q Consensus 56 ~p~~~~~V~Is~~vLlkIl~Ha~~~--~p~EV~GlLLG~~~~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r 133 (360)
....++.|.|.....-..++-|++. -..|.||+|.|+...+.+.||+...--.+++.+.|++..+.. ..+..
T Consensus 247 ~~k~lr~v~ip~~l~~~Fl~la~~NT~knlETCGiL~g~L~~n~f~IThliiPkQeatsd~C~t~neee--lF~vQ---- 320 (424)
T KOG2880|consen 247 EGKILRDVHIPERLMEVFLQLAKSNTKKNLETCGILAGKLERNEFYITHLIIPKQEATSDSCNTMNEEE--LFEVQ---- 320 (424)
T ss_pred CCccceEEEecHHHHHHHHHHHhhcccccchHHHHhhhHhhcCcEEEEEEEeecccCCCccccccCHHH--Hheec----
Confidence 4556889999999999999999863 568999999999999999999987555677888887755432 12211
Q ss_pred HhCCCCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccC
Q 018129 134 QAGRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPE 199 (360)
Q Consensus 134 ~v~~~e~vVGWYHSHP~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~t~~~G~v~ikAFRl~p~ 199 (360)
...++-.+||-||||..+||+|.+|++|+++||.|.|.+||||+.|... .-|-||+++.
T Consensus 321 -dq~~L~tlGWIHTHPTQt~FmSSVDlHTHcSYQiMlPEAiAIV~aPk~~------~tGiFrLt~~ 379 (424)
T KOG2880|consen 321 -DQHELLTLGWIHTHPTQTCFMSSVDLHTHCSYQIMLPEAIAIVCAPKSK------TTGIFRLTDP 379 (424)
T ss_pred -ccccceeeeeeecCCccchhheeccccccceeeeecchheeEEeccccC------CcceEEecCC
Confidence 2356789999999999999999999999999999999999999999743 4677999843
No 24
>cd08073 MPN_NLPC_P60 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains. This family contains bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains at the N-terminus of NlpC/P60 phage tail protein domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=99.44 E-value=1e-12 Score=110.17 Aligned_cols=94 Identities=16% Similarity=0.095 Sum_probs=70.3
Q ss_pred HHHHHHHHHhcCCCceeEEEeeeEecCCeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCCCCceEEEEecC
Q 018129 69 ALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAVGWYHSH 148 (360)
Q Consensus 69 vLlkIl~Ha~~~~p~EV~GlLLG~~~~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~~e~vVGWYHSH 148 (360)
++-.|+.||+++.|.|+||+|+|.. .++..++++|...+.+..+..++.+|.. ..+ ...+||.||||
T Consensus 2 i~~~i~~ha~~~~P~E~CGll~g~~-----~~~~~~p~~N~~~~p~~~F~idp~e~~~----a~~----~~~ivgi~HSH 68 (108)
T cd08073 2 LEDAILAHAKAEYPREACGLVVRKG-----RKLRYIPCRNIAADPEEHFEISPEDYAA----AED----EGEIVAVVHSH 68 (108)
T ss_pred HHHHHHHHHhHCCCCcceEEEEecC-----CceEEEECccCCCCccceEEeCHHHHHH----Hhc----CCCEEEEEEcC
Confidence 4668999999999999999999965 2456688887654443445556666433 222 22899999999
Q ss_pred CCCCCccCHHhHHHHHhhhhcCCCeEEEEEcC
Q 018129 149 PGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDP 180 (360)
Q Consensus 149 P~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp 180 (360)
|+..+.||..|+.. ...++.++||++.
T Consensus 69 P~~~a~PS~~D~~~-----~~~~~~~~iIvs~ 95 (108)
T cd08073 69 PDGSPAPSEADRAQ-----QEATGLPWIIVSW 95 (108)
T ss_pred CCCCCCCCHHHHHH-----hhcCCCcEEEEEc
Confidence 99999999999853 2347889999995
No 25
>cd08060 MPN_UPF0172 Mov34/MPN/PAD-1 family: UPF0172 family of unknown function includes neighbor of COX4 (Noc4p). This family includes Noc4p (neighbor of COX4; neighbor of Cytochrome c Oxidase 4; nucleolar complex associated 4 homolog) which belongs to the family of unknown function, UPF0172, with MPN/JAMM-like domains. Proteins in this family are homologs of the NOC4 gene which is conserved in eukaryotic members including human, dog, mouse, rat, chicken, zebrafish, fruit fly, mosquito, S.pombe, K.lactis, E.gossypii, M.grisea, N.crassa, A.thaliana, and rice. NOC4 highly expressed in the pancreas and moderately in liver, heart, lung, kidney, brain, skeletal muscle, and placenta. This nucleolar protein forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.
Probab=99.30 E-value=3.7e-11 Score=109.59 Aligned_cols=110 Identities=20% Similarity=0.176 Sum_probs=76.0
Q ss_pred ECHHHHHHHHHHHhcCCCceeEEEeeeEec-CCeEEEEEEEeCCcccCCCccccccChHH--HHHHHHHHHHHhCCCCce
Q 018129 65 ISALALLKMVVHARSGGTIEVMGLMQGKTD-GDAIIVMDAFALPVEGTETRVNAQADAYE--YMVDYSQTNKQAGRLENA 141 (360)
Q Consensus 65 Is~~vLlkIl~Ha~~~~p~EV~GlLLG~~~-~~~leVtd~F~lP~~~te~~v~~~~e~~e--y~~~ml~~~r~v~~~e~v 141 (360)
|+..++.||+.||....+.||||+|+|+.. ++++.|++++|+.+.. ... ++.. -+....+.+++ .++.|
T Consensus 1 is~~ay~ki~~HA~k~p~~evcGlLlG~~~~~~~~~V~d~vPl~h~~----~~l--~P~~Eval~~ve~~~~~--~gl~I 72 (182)
T cd08060 1 LSTLAYVKMLLHAAKYPHCAVNGLLLGKKSSGGSVEITDAVPLFHSC----LAL--APMLEVALALVDAYCKS--SGLVI 72 (182)
T ss_pred CCHHHHHHHHHHHHHcCCchheEEEEeeecCCCCEEEEEEEEcCCCc----ccc--CHHHHHHHHHHHHHHHH--CCCEE
Confidence 467899999999999777899999999987 7789999999999842 223 3322 12334555665 46899
Q ss_pred EEEEecCCCCCC-ccCHHhHHHHHhhhhcCCCeEEEEEcCCC
Q 018129 142 VGWYHSHPGYGC-WLSGIDVSTQMLNQQFQEPFLAVVIDPTR 182 (360)
Q Consensus 142 VGWYHSHP~~g~-~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~ 182 (360)
||+|||||.++. -|+.+=...-..-+...+.++.+++|-.+
T Consensus 73 vG~Yhsh~~~~d~~~~~~a~kIadki~~~~~~a~ll~vdn~~ 114 (182)
T cd08060 73 VGYYQANERLDDSSPSPVAKKIADKIAENFSNACLLMVDNEK 114 (182)
T ss_pred EEEEecCCcccCCCCcHHHHHHHHHHHHhCCCCEEEEEeCcc
Confidence 999999997642 33332111111122345678888898654
No 26
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=99.27 E-value=1.9e-11 Score=100.10 Aligned_cols=95 Identities=22% Similarity=0.295 Sum_probs=62.9
Q ss_pred HHHHHHHHHHHhcCCCceeEEEeeeEecCCeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCCCCceEEEEe
Q 018129 67 ALALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAVGWYH 146 (360)
Q Consensus 67 ~~vLlkIl~Ha~~~~p~EV~GlLLG~~~~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~~e~vVGWYH 146 (360)
..++.+|+.|++...|.|+||+|+|......+.++...... +.++.. +... +....+..+||+||
T Consensus 2 ~~~~~~i~~~~~~~~p~E~~G~L~g~~~~~~~~~~~~~~~~-------------p~~~~~-~~~~-~~~~~~~~~vg~~H 66 (104)
T PF14464_consen 2 EEVLEQIIAHARAAYPNEACGLLLGRRDDQRFIVVPNVNPD-------------PRDSFR-RERF-EARERGLEIVGIWH 66 (104)
T ss_dssp -HHHHHHHHHHHHHTTS-EEEEEEEEEECCEEEEEEEEE---------------HHCHHH-HHH--HHHHHT-EEEEEEE
T ss_pred HHHHHHHHHHHhhCCCCeEEEEEEEEecCCEEEEEeCCCCC-------------cHHHHH-HHhh-hhhcccceeeEEEE
Confidence 35788999999999999999999999977777777665411 111111 1110 12235689999999
Q ss_pred cCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcC
Q 018129 147 SHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDP 180 (360)
Q Consensus 147 SHP~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp 180 (360)
|||+.+++||..|+..... ..++++||+..
T Consensus 67 SHP~~~a~pS~~D~~~~~~----~~~~~~iI~~~ 96 (104)
T PF14464_consen 67 SHPSGPAFPSSTDIRSMRD----LAPPSYIIVGN 96 (104)
T ss_dssp EESSSSSS--HHHHHTHCC----S-SCEEEEEEE
T ss_pred cCCCCCCCCCHHHHHhhhc----cCCeEEEEEeC
Confidence 9999999999999876421 11678888874
No 27
>cd08056 MPN_PRP8 Mpr1p, Pad1p N-terminal (MPN) domains without isopeptidase activity found in splicing factor Prp8. Members of this family are found in pre-mRNA-processing factor 8 (Prp8) which is a critical splicing factor, interacting with several other spliceosomal proteins, snRNAs, and the pre-mRNA, thus organizing and stabilizing the spliceosome catalytic core. Prp8 is one of the largest and most highly conserved of nuclear proteins, occupying a central position in the catalytic core of the spliceosome. Its C-terminal domain exhibits a JAB1/MPN-like core similar to deubiquitinating enzymes, but does not show catalytic isopeptidase activity, possibly because the putative isopeptidase center is covered by insertions and terminal appendices that are grafted onto this core, thus impairing the metal binding site. It is proposed that this domain is a protein interaction domain instead of a Zn(2+)-dependent metalloenzyme as proposed for some MPN proteins. The DEAD-box protein Brr2 and t
Probab=99.16 E-value=3.9e-10 Score=107.39 Aligned_cols=126 Identities=21% Similarity=0.264 Sum_probs=104.3
Q ss_pred EEEECHHHHHHHHHHHhcCCCceeEEEeeeEecC---CeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCCC
Q 018129 62 RVKISALALLKMVVHARSGGTIEVMGLMQGKTDG---DAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRL 138 (360)
Q Consensus 62 ~V~Is~~vLlkIl~Ha~~~~p~EV~GlLLG~~~~---~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~~ 138 (360)
++.|+..+|-|.+.-|.. ..++||.|.|+... +..+|+-..-.|+.++.+.|.+..+..+ .+. + .+
T Consensus 37 t~vlPknllkkFi~iaD~--rtQ~~GyLyG~~~~d~~~vkeI~cIvipPQ~gt~~sv~l~~~~~~--~~~---l----~~ 105 (252)
T cd08056 37 TYILPKNLLKKFISISDL--RTQIAGYLYGKSPPDNPQVKEIRCIVLVPQLGTHQTVTLPQQLPQ--HEY---L----ED 105 (252)
T ss_pred EEEeCHHHHHHHHHHhhh--cceEEEEEeccCCCCCCCeEEEEEEEECCEeCCcCcEECCccCcc--chh---h----CC
Confidence 788999999999988864 46999999999754 6789998888899998888877443212 111 1 35
Q ss_pred CceEEEEecCCCCCCccCHHhHHHHHhhhhcCC-----CeEEEEEcCCCCccCCeeeEEEEEEccCCCC
Q 018129 139 ENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQE-----PFLAVVIDPTRTVSAGKVEIGAFRTYPEGYK 202 (360)
Q Consensus 139 e~vVGWYHSHP~~g~~~S~iDI~tQ~~yQ~~~~-----p~V~LVvDp~~t~~~G~v~ikAFRl~p~~~~ 202 (360)
+..+||-||||.-.+++|..||.+|+.+|...+ .+|.+++++. .|.++++||+++++|+.
T Consensus 106 Le~LGWIHTqp~e~~~Lss~Dv~tha~~~~~~~~w~~~~~V~it~Sft----pGs~sl~ay~LT~~G~~ 170 (252)
T cd08056 106 LEPLGWIHTQPNELPQLSPQDVTTHAKILADNPSWDGEKTVILTCSFT----PGSCSLTAYKLTPEGYE 170 (252)
T ss_pred CEeeEEEEcCCCCccccCHHHHHHHHHHHHhccccCCCcEEEEEEcCC----CCceEEEEEecCHHHHH
Confidence 889999999999899999999999999999876 7899999974 68899999999988754
No 28
>cd08059 MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); prokaryotic. This family contains bacterial and archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These catalytically active domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=98.90 E-value=1.1e-08 Score=83.87 Aligned_cols=91 Identities=24% Similarity=0.290 Sum_probs=65.6
Q ss_pred HHHHHHHHHhcCCCceeEEEeeeEecCCeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCCCCceEEEEecC
Q 018129 69 ALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAVGWYHSH 148 (360)
Q Consensus 69 vLlkIl~Ha~~~~p~EV~GlLLG~~~~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~~e~vVGWYHSH 148 (360)
++..|..|++...|.|+||+|+|...+ .++++..+|+.. .+. .+.. .+.+. ..+..+||.||||
T Consensus 2 ~~~~i~~~~~~~~p~E~~gll~~~~~~---~~~~~~~~~~~~----~~~--~~~~-----~~~a~--~~~~~~v~i~HsH 65 (101)
T cd08059 2 LLKTILVHAKDAHPDEFCGFLSGSKDN---VMDELIFLPFVS----GSV--SAVI-----DLAAL--EIGMKVVGLVHSH 65 (101)
T ss_pred HHHHHHHHHHhcCChhhheeeecCCCC---eEEEEEeCCCcC----Ccc--ChHH-----HHHHh--hCCCcEEEEEecC
Confidence 566789999999999999999997543 677888888532 112 1211 22222 3457899999999
Q ss_pred CCCCCccCHHhHHHHHhhhhcCCCeEEEEEcC
Q 018129 149 PGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDP 180 (360)
Q Consensus 149 P~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp 180 (360)
|+..+.||..|+.... .....++|+..
T Consensus 66 P~g~~~PS~~D~~~~~-----~~~~~~iIv~~ 92 (101)
T cd08059 66 PSGSCRPSEADLSLFT-----RFGLYHVIVCY 92 (101)
T ss_pred cCCCCCCCHHHHHHHH-----hcCCeEEEEEC
Confidence 9999999999987422 23678888864
No 29
>TIGR02256 ICE_VC0181 integrative and conjugative element protein, VC0181 family. This uncharacterized protein is found in several Proteobacteria, among them Rhizobium sp. NGR234, Vibrio cholerae, Myxococcus xanthus, and E. coli strain ECOR31. In the latter, it is part of an integrative and conjugative element that is readily induced to excise and circularize.
Probab=98.88 E-value=2.8e-08 Score=86.19 Aligned_cols=109 Identities=17% Similarity=0.199 Sum_probs=71.2
Q ss_pred HHHHHHHHh--cCCCceeEEEeeeEecCCeEEEEEEEeCCcc-cCCCccccccChHHHHHHHHHHHHHhCCCCceEEEEe
Q 018129 70 LLKMVVHAR--SGGTIEVMGLMQGKTDGDAIIVMDAFALPVE-GTETRVNAQADAYEYMVDYSQTNKQAGRLENAVGWYH 146 (360)
Q Consensus 70 LlkIl~Ha~--~~~p~EV~GlLLG~~~~~~leVtd~F~lP~~-~te~~v~~~~e~~ey~~~ml~~~r~v~~~e~vVGWYH 146 (360)
+++++..++ ...+.|.+|+|+|...+..+.|+++- .|.. ...++..+.......+...-+..++.+.....||=||
T Consensus 2 v~~~~~~~~Q~~~~~~EtGGiLiG~~~~~~~ii~~~t-~P~p~d~~tr~~F~r~~~~~q~~i~~~~~~s~g~~~ylGeWH 80 (131)
T TIGR02256 2 VVAMLKSYRQWHDLSTETGGVLIGERRGAHAVITKIS-EPGSGDIRTRKRFSRDGEHHQSEVDEHFEVSGGVDTYLGEWH 80 (131)
T ss_pred HHHHHHHHHhCcCCCCccceEEEEEEcCCcEEEEEEE-cCCCCcccCceEEEeCcHHHHHHHHHHHHHhCCceEEEEecC
Confidence 344555444 34578999999999988888888865 3332 2233444443333334444455555555689999999
Q ss_pred cCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEc
Q 018129 147 SHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVID 179 (360)
Q Consensus 147 SHP~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvD 179 (360)
|||...+.||.+|+.+-...=+...+.+.||+-
T Consensus 81 tHP~~~p~PS~~D~~~~~~~~~~~~~~l~iIvG 113 (131)
T TIGR02256 81 THPEDQPEPSWTDRRSWRTIIRSPEAMLLLIVG 113 (131)
T ss_pred cCCCCCCCCCHHHHHHHHHHHhCCCeeEEEEEc
Confidence 999988899999998754332234456666665
No 30
>TIGR03735 PRTRC_A PRTRC system protein A. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated protein A.
Probab=98.74 E-value=2.6e-08 Score=91.45 Aligned_cols=112 Identities=20% Similarity=0.117 Sum_probs=77.9
Q ss_pred EECHHHHHHHHHHHhcCCCceeEEEeeeEecCCeEEEEEEEeCCcccC-CCccccccChHHHHHHHHHHHHHhCCCCceE
Q 018129 64 KISALALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGT-ETRVNAQADAYEYMVDYSQTNKQAGRLENAV 142 (360)
Q Consensus 64 ~Is~~vLlkIl~Ha~~~~p~EV~GlLLG~~~~~~leVtd~F~lP~~~t-e~~v~~~~e~~ey~~~ml~~~r~v~~~e~vV 142 (360)
+|....+-+|+.||+++.|.|+||++.|...+.. ..++++.+... .+.+.+ +. .| ..+++.+|
T Consensus 74 ~Ip~~l~~~ii~hAr~~~P~EacG~Iag~~~~~~---~r~~p~~N~~~Sp~~~~~--d~-----~~------~~~ge~lV 137 (192)
T TIGR03735 74 PIPASLLEEFAEAARAALPNEVAAWIVWNSETGS---LRLAALESIEASPGHIDY--RR-----PR------LDDGEHLV 137 (192)
T ss_pred CCCHHHHHHHHHHHHhcCCcceEEEEEEcCCCCE---EEEEeccccccCCceEEE--cc-----hH------HhCCCeEE
Confidence 8999999999999999999999999999633333 35577776432 233333 21 11 14689999
Q ss_pred EEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCC
Q 018129 143 GWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEG 200 (360)
Q Consensus 143 GWYHSHP~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~t~~~G~v~ikAFRl~p~~ 200 (360)
+.|||||..+++||.+|+..- ..+--++.|+--.. ++..++ +||+.-.|
T Consensus 138 ~iyHSH~~spA~PS~tD~~Dd-----~~~~k~~~ViG~~~---~~~p~~-~~Rl~~~G 186 (192)
T TIGR03735 138 VDLHSHGTGSAFFSETDDADD-----KGEVKISGVLGCLD---QGTPQA-VFRLCLLG 186 (192)
T ss_pred EEEcCCCCCCCCCCcccchhh-----cCceEEEEEEEecC---CCCceE-EEEEEecc
Confidence 999999999999999998631 12245777775432 333443 57876543
No 31
>KOG3050 consensus COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=98.49 E-value=2.5e-07 Score=87.09 Aligned_cols=160 Identities=21% Similarity=0.294 Sum_probs=107.6
Q ss_pred EEEECHHHHHHHHHHHh-----cCCCc-eeEEEeeeEecCCeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHh
Q 018129 62 RVKISALALLKMVVHAR-----SGGTI-EVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQA 135 (360)
Q Consensus 62 ~V~Is~~vLlkIl~Ha~-----~~~p~-EV~GlLLG~~~~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v 135 (360)
+|.++|+|++.|-+|.- .+.|. .|.|.|+|+..|..+||+|+|-+-..-.++..-++ .+|...=.+..++|
T Consensus 10 tv~LHPLVImniSdH~tR~k~Q~gpp~~~VyGaliG~Q~GR~vEi~NSFeL~~d~~~~~~~~d---ke~l~kk~eqykqV 86 (299)
T KOG3050|consen 10 TVKLHPLVIMNISDHYTRVKTQLGPPVKQVYGALIGKQRGRNVEIMNSFELKMDTEEDTETID---KEYLEKKEEQYKQV 86 (299)
T ss_pred eEEeccEEEEehhHHHHHHHhhcCCcHHHhhhhheecccCceEEEeeeeEEEecchhhhhhcc---HHHHHHHHHHHHHh
Confidence 68999999999999984 35566 89999999999999999999998654322221122 35666667778889
Q ss_pred CCCCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCc-cCCeeeEEEEEEccCCCCCCCCCCCccccc
Q 018129 136 GRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTV-SAGKVEIGAFRTYPEGYKPPDEPISEYQTI 214 (360)
Q Consensus 136 ~~~e~vVGWYHSHP~~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~t~-~~G~v~ikAFRl~p~~~~~~~~~~~e~~~i 214 (360)
=++..++|||.++.+ +-||.+.|..|.. ...+-.++|-..|...- ...++.+=+|-+.
T Consensus 87 Fpdl~vlGwYttG~d--~t~sd~~i~k~l~--~i~esplflkLNp~t~~t~~~pv~lfese~d----------------- 145 (299)
T KOG3050|consen 87 FPDLYVLGWYTTGSD--PTPSDIHIHKQLM--DINESPLFLKLNPATNHTDKDPVTLFESEID----------------- 145 (299)
T ss_pred cccceEEEEeecCCC--CChhhhHHHHHHH--hhhcCceEEEecchhccccCCCceeeeeehe-----------------
Confidence 999999999998763 4566665555443 24566788888885321 1112333332221
Q ss_pred chhhhhhhcCccceeEEeeEEEecChhHHHHHHHHh
Q 018129 215 PLNKIEDFGVHCKQYYSLDITYFKSSLDCHLLDLLW 250 (360)
Q Consensus 215 p~~ki~d~g~~~~~fyeLpV~i~~s~l~~~~L~~L~ 250 (360)
.+. |..--.|.++.-.+-.-..+|...+-..
T Consensus 146 ---vid--g~~q~~f~~~tytl~teEaERIgVdHVA 176 (299)
T KOG3050|consen 146 ---VID--GEAQMLFVPLTYTLATEEAERIGVDHVA 176 (299)
T ss_pred ---eec--CcceeeeeeeEEEEeehhhhhccchhhe
Confidence 111 1123467777777777778887777653
No 32
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=98.37 E-value=8.7e-06 Score=75.29 Aligned_cols=114 Identities=20% Similarity=0.172 Sum_probs=74.3
Q ss_pred EEEECHHHHHHHHHHHhcCCCceeEEEeeeEecCCe--EEEEEEEeCCcccCCCccccccChHHHHHHHH-HHHHHhCCC
Q 018129 62 RVKISALALLKMVVHARSGGTIEVMGLMQGKTDGDA--IIVMDAFALPVEGTETRVNAQADAYEYMVDYS-QTNKQAGRL 138 (360)
Q Consensus 62 ~V~Is~~vLlkIl~Ha~~~~p~EV~GlLLG~~~~~~--leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml-~~~r~v~~~ 138 (360)
.|.|+..++.||+-||-.-...-|+|+|+|...++. +.|+||.|+-+....- .. -.|--...+ ..++ ..+
T Consensus 3 ~v~is~~AY~K~~LHaaKyP~~aVnGvLlg~~~~~~~~v~i~DaVPLfH~~~~L--~P---mlEvAL~qvd~~~~--~~g 75 (196)
T PF03665_consen 3 SVEISSRAYAKMILHAAKYPHCAVNGVLLGKSSKSSSEVEIVDAVPLFHHWLSL--SP---MLEVALAQVDAYAK--SNG 75 (196)
T ss_pred eEEEcHHHHHHHHHHhccCCCCceeeEEEeccCCCCceEEEeeceeccccccCc--ch---HHHHHHHHHHHHHh--hCC
Confidence 689999999999999998666899999999987554 9999999998843221 11 111111112 2233 246
Q ss_pred CceEEEEecCCCCC-CccCHHhHHHHHhhhhcCCCeEEEEEcCCC
Q 018129 139 ENAVGWYHSHPGYG-CWLSGIDVSTQMLNQQFQEPFLAVVIDPTR 182 (360)
Q Consensus 139 e~vVGWYHSHP~~g-~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~ 182 (360)
+.|||+||....+. .-|+.+=...-..-+...+.++.|++|-.+
T Consensus 76 l~IvGyY~Ane~~~d~~~~~~a~kiad~I~~~~~~a~ll~idn~k 120 (196)
T PF03665_consen 76 LVIVGYYQANERLDDNSPSPVAEKIADKIAENFSDACLLMIDNKK 120 (196)
T ss_pred CEEEEEEEeccccccCCCCHHHHHHHHHHHhhCCCcEEEEEECcc
Confidence 99999999987542 234443111111112245778889999654
No 33
>cd08061 MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain. Npl4p (nuclear protein localization-4) is identical to Hmg-CoA reductase degradation 4 (HRD4) protein and contains a domain that is part of the pfam clan MPN/Mov34-like. Npl4 plays an intermediate role between endoplasmic reticulum-associated degradation (ERAD) substrate ubiquitylation and proteasomal degradation. Npl4p associates with Cdc48p (Cdc48 in yeast and p97 or valosin-containing protein (VCP) in higher eukaryotes), the highly conserved ATPase of the AAA family, via ubiquitin fusion degradation-1 protein (Ufd1p) to form a Cdc48p-Ufd1p-Npl4p complex which then functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.
Probab=98.27 E-value=3e-05 Score=75.20 Aligned_cols=136 Identities=18% Similarity=0.289 Sum_probs=103.7
Q ss_pred CCeeEEEECHHHHHHHHHH-HhcCCCceeEEEeeeEecCC-------eEEEEEEEeCCcccCCCccccccChHHHHHHHH
Q 018129 58 HYFKRVKISALALLKMVVH-ARSGGTIEVMGLMQGKTDGD-------AIIVMDAFALPVEGTETRVNAQADAYEYMVDYS 129 (360)
Q Consensus 58 ~~~~~V~Is~~vLlkIl~H-a~~~~p~EV~GlLLG~~~~~-------~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml 129 (360)
+.+.+|.+....++.-..+ +.......-||.|.|+.... .++|.-.+--|+.++.+.+.+..+.. +...-
T Consensus 8 r~Vd~vef~~~~~~~~f~~~~w~~~~~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~d~~--~~~vd 85 (274)
T cd08061 8 RHVDHVEFDNPSIVEFFLYVFWRKTGQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPN--ADTVD 85 (274)
T ss_pred CCcCEEEEecHHHHHHHHHHHHHhhcceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEccchh--hhHHH
Confidence 3567788887777766666 54445678899999998654 57777778888888887776654432 22223
Q ss_pred HHHHHhCCCCceEEEEecCCCC----CCccCHHhHHHHHhhhh------cCCCeEEEEEcCCCCccCCeeeEEEEEEccC
Q 018129 130 QTNKQAGRLENAVGWYHSHPGY----GCWLSGIDVSTQMLNQQ------FQEPFLAVVIDPTRTVSAGKVEIGAFRTYPE 199 (360)
Q Consensus 130 ~~~r~v~~~e~vVGWYHSHP~~----g~~~S~iDI~tQ~~yQ~------~~~p~V~LVvDp~~t~~~G~v~ikAFRl~p~ 199 (360)
+.+. ..++..|||-.||+.- ++++|...|...+.+|. +...||-+|++|.. .|.+.+.||+++..
T Consensus 86 ~iA~--~lGL~~VG~IfT~l~~~~~d~~~LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~---~g~i~~~ayQvSdq 160 (274)
T cd08061 86 AIAA--ALGLERVGWIFTDLPREDKDGYFLSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDK---DGQIHFEAYQVSDQ 160 (274)
T ss_pred HHHH--HcCCeEEEEEEecCCCCCCCceeECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCC---CCceeeeeeeecHH
Confidence 3343 3569999999999966 78999999999999995 67899999999975 58999999999875
Q ss_pred C
Q 018129 200 G 200 (360)
Q Consensus 200 ~ 200 (360)
+
T Consensus 161 ~ 161 (274)
T cd08061 161 A 161 (274)
T ss_pred H
Confidence 3
No 34
>KOG3289 consensus Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only]
Probab=97.52 E-value=0.0016 Score=59.08 Aligned_cols=114 Identities=23% Similarity=0.248 Sum_probs=74.8
Q ss_pred EEEECHHHHHHHHHHHhcCCCceeEEEeeeEe--cCCeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCCCC
Q 018129 62 RVKISALALLKMVVHARSGGTIEVMGLMQGKT--DGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLE 139 (360)
Q Consensus 62 ~V~Is~~vLlkIl~Ha~~~~p~EV~GlLLG~~--~~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~~e 139 (360)
.|+|++.++.||+-||-.-...-|-|+|+|.. .|+.++|+||.|+-++... . ....|-...+++..- +..+.
T Consensus 3 ~veis~~aY~kmiLH~akyph~aVnGLLla~~~~kg~~v~itdcVPLfH~~la----L-aPmlEvAl~lId~~~-~~~Gl 76 (199)
T KOG3289|consen 3 EVEISALAYVKMILHAAKYPHAAVNGLLLAPATGKGECVEITDCVPLFHSHLA----L-APMLEVALNLIDVWG-AQAGL 76 (199)
T ss_pred ceeehhhHHHHHHHHhccCcccceeeEEEeccCCCCCeEEEEecchhhccccc----c-ccHHHHHHHHHHHHH-HhcCe
Confidence 58999999999999998865668999999965 4678999999999876421 1 112343333444322 24579
Q ss_pred ceEEEEecCCCCCC-ccCHHhHHHHHhhhhcCCCeEEEEEcCC
Q 018129 140 NAVGWYHSHPGYGC-WLSGIDVSTQMLNQQFQEPFLAVVIDPT 181 (360)
Q Consensus 140 ~vVGWYHSHP~~g~-~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~ 181 (360)
.|+|.||+--.+.- -+.+.-...-..-+.+.+....|++|-.
T Consensus 77 viaGyy~Ane~~~D~s~~~~A~kiadrIse~f~~A~ilv~dn~ 119 (199)
T KOG3289|consen 77 VIAGYYHANERVNDQSLNPVALKIADRISEFFPDAAILVLDNK 119 (199)
T ss_pred EEEEEeecCCCccccCccHHHHHHHHHHHhhCCCCeEEEEecc
Confidence 99999998865422 2222211111123456677788888854
No 35
>PF05021 NPL4: NPL4 family; InterPro: IPR007717 The HRD4 gene is identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterised step in ER-associated degradation following ubiquitination of target proteins but preceding their recognition by the 26S proteasome []. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing [].
Probab=97.36 E-value=0.0026 Score=62.70 Aligned_cols=108 Identities=16% Similarity=0.258 Sum_probs=81.9
Q ss_pred EEEeeeEecCC-------eEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCCCCceEEEEecCCC--------
Q 018129 86 MGLMQGKTDGD-------AIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAVGWYHSHPG-------- 150 (360)
Q Consensus 86 ~GlLLG~~~~~-------~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~~e~vVGWYHSHP~-------- 150 (360)
+|.|.|..+.. ..+|.-.+--|++++.+.+....+.. ....-+.++. -|+..|||-=||+.
T Consensus 2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~~~d~~~l~~d~~--~~~vd~iA~~--lGL~rVG~IfTdl~~~~~~~g~ 77 (306)
T PF05021_consen 2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEGEPDGFTLLPDEN--EERVDAIASA--LGLERVGWIFTDLTDDGSGDGT 77 (306)
T ss_pred eEEEEEEEeccCCCCCceEEEEEEEECCCcCCCCCCEEEcCCcc--HHHHHHHHHH--CCCEEEEEEEecCcccccCCCc
Confidence 79999998643 46777788889988888777644432 2333444443 46999999999986
Q ss_pred -------CCCccCHHhHHHHHhhhhc-------------CCCeEEEEEcCCCCccCCeeeEEEEEEccCC
Q 018129 151 -------YGCWLSGIDVSTQMLNQQF-------------QEPFLAVVIDPTRTVSAGKVEIGAFRTYPEG 200 (360)
Q Consensus 151 -------~g~~~S~iDI~tQ~~yQ~~-------------~~p~V~LVvDp~~t~~~G~v~ikAFRl~p~~ 200 (360)
-..++|...|..-+.+|.. ...||-+|+++.. .|.+.+.||+++...
T Consensus 78 v~~~r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~s~~g~fgSkFVT~vvsg~~---~g~i~~~ayQvS~q~ 144 (306)
T PF05021_consen 78 VKCKRHKDSYFLSSLEIIFAAKLQNKHPNPCKYSETGYFGSKFVTCVVSGDE---EGEIHFEAYQVSNQC 144 (306)
T ss_pred eeeccccccccccHHHHHHHHHHHHhcCccccccCCCccCCeEEEEEEeCCC---CCceeeEEeeehHHH
Confidence 5689999999887888863 3568999999863 789999999998743
No 36
>KOG1795 consensus U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=82.98 E-value=3.1 Score=48.05 Aligned_cols=110 Identities=18% Similarity=0.225 Sum_probs=75.5
Q ss_pred CCCceeEEEeeeEec---CCeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCCCCceEEEEecCCCCCCccC
Q 018129 80 GGTIEVMGLMQGKTD---GDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAVGWYHSHPGYGCWLS 156 (360)
Q Consensus 80 ~~p~EV~GlLLG~~~---~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~~e~vVGWYHSHP~~g~~~S 156 (360)
.....+.|+|.|.-- +..-+|.-..-+|+-++-..|+....--. .. +-.+...+||-||-|.-=.++|
T Consensus 2112 D~r~qiag~~yG~s~~d~pqvkeIr~ivmvPQ~gs~~~v~lp~~lP~--~~-------~l~d~e~Lgw~hTq~~el~~ls 2182 (2321)
T KOG1795|consen 2112 DLRTQIAGYLYGVSPPDNPQVKEIRCIVMVPQWGSHQGVHLPSFLPI--HG-------VLEDLEPLGWIHTQPNELPQLS 2182 (2321)
T ss_pred chhhhhheeeeccCCCCCCccceEEEEEeccccccccccccCccCCc--ch-------hccCCcccchhhcCccccccCC
Confidence 345678899999753 33457776666787776555554211000 11 1245788999999998888999
Q ss_pred HHhHHHHHh-hhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCCCC
Q 018129 157 GIDVSTQML-NQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEGYK 202 (360)
Q Consensus 157 ~iDI~tQ~~-yQ~~~~p~V~LVvDp~~t~~~G~v~ikAFRl~p~~~~ 202 (360)
..||.++.- .+.....+|.|.++- ..|.+++.||.++|+||.
T Consensus 2183 p~dV~th~ki~~~~k~k~i~~t~~~----tpgs~sl~ay~lt~~G~e 2225 (2321)
T KOG1795|consen 2183 PQDVTTHAKILVDNKEKCIIITCSF----TPGSCSLTAYKLTPSGYE 2225 (2321)
T ss_pred HHHhhhhhhhhhcCccceEEEEeec----cCCcceeeeeccCccccc
Confidence 999998763 222335677777763 379999999999999975
No 37
>KOG2834 consensus Nuclear pore complex, rNpl4 component (sc Npl4) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=61.75 E-value=1e+02 Score=32.53 Aligned_cols=132 Identities=17% Similarity=0.279 Sum_probs=84.7
Q ss_pred eeEEEEC-HHHHHHHHHHHhcCCCceeEEEeeeEecCC-eE------EEEEEEeCCcccCCCccccccChHHHHHHHHHH
Q 018129 60 FKRVKIS-ALALLKMVVHARSGGTIEVMGLMQGKTDGD-AI------IVMDAFALPVEGTETRVNAQADAYEYMVDYSQT 131 (360)
Q Consensus 60 ~~~V~Is-~~vLlkIl~Ha~~~~p~EV~GlLLG~~~~~-~l------eVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~ 131 (360)
+..|.++ +.++-..++-.|.. ...-.|+|.|...+. .+ +|.-.|--|+.+.++.+.+.. ..+ +..+-+.
T Consensus 174 vD~VeFd~~~~v~~Fl~~wr~s-g~QR~GflyG~y~e~~~vPLGika~V~aIYEPPQ~~~~dgl~l~~-~~e-~~~vD~~ 250 (510)
T KOG2834|consen 174 VDHVEFDNAELVNHFLNEWRAS-GVQRFGFLYGRYTEHGNVPLGIKAVVAAIYEPPQHGEEDGLELLE-DDE-AKRVDAI 250 (510)
T ss_pred cceEeecchHHHHHHHHHHHHh-hhhhcceEEEeecccccccccceeeEEEEecCCccCCcCCeEEec-cch-hhhHHHH
Confidence 3345554 33444555555544 345569999998532 33 777788889988888876642 222 2222222
Q ss_pred HHHhCCCCceEEEEecCC---------------CCCCccCHHhHHHHHhhhhcCC-------------CeEEEEEcCCCC
Q 018129 132 NKQAGRLENAVGWYHSHP---------------GYGCWLSGIDVSTQMLNQQFQE-------------PFLAVVIDPTRT 183 (360)
Q Consensus 132 ~r~v~~~e~vVGWYHSHP---------------~~g~~~S~iDI~tQ~~yQ~~~~-------------p~V~LVvDp~~t 183 (360)
+ .+.++..|||--+-- .-+.|+|...+.+-+.+|..-| .+|-+|+.-..
T Consensus 251 a--~~lGLrRVG~IFTDl~~~~s~egtV~~~rhkdsyFLSseE~~~aa~~Q~~hpn~~~~s~~~~fgSkfVT~visg~~- 327 (510)
T KOG2834|consen 251 A--EGLGLRRVGWIFTDLVTADSAEGTVHYKRHKDSYFLSSEECITAAMFQNKHPNICEWSRDGHFGSKFVTLVISGDL- 327 (510)
T ss_pred H--HhcCceeeEEEEeeeecccCccceEEeeeccchhcccHHHHHHHhhhhhcCCchheeeccccccceeEEEEEecCC-
Confidence 3 356799999964322 1256999999988788886532 36777886543
Q ss_pred ccCCeeeEEEEEEccC
Q 018129 184 VSAGKVEIGAFRTYPE 199 (360)
Q Consensus 184 ~~~G~v~ikAFRl~p~ 199 (360)
.|.+.+-.|+.+..
T Consensus 328 --~~~V~f~~YQVSnq 341 (510)
T KOG2834|consen 328 --DGEVHFEGYQVSNQ 341 (510)
T ss_pred --CcceeeeeeehhHH
Confidence 67899999998653
No 38
>cd08071 MPN_DUF2466 Mov34/MPN/PAD-1 family. Mov34 DUF2466 (also known as DNA repair protein RadC) domain of unknown function contains the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. However, to date, the name RadC has been misleading and no function has been determined.
Probab=40.04 E-value=2.2e+02 Score=23.75 Aligned_cols=25 Identities=24% Similarity=0.110 Sum_probs=22.1
Q ss_pred CCceEEEEecCCCCCCccCHHhHHH
Q 018129 138 LENAVGWYHSHPGYGCWLSGIDVST 162 (360)
Q Consensus 138 ~e~vVGWYHSHP~~g~~~S~iDI~t 162 (360)
+..-|..-|.||...+.||..|+..
T Consensus 59 ~A~~vil~HNHPsG~~~PS~~D~~~ 83 (113)
T cd08071 59 NAAAIILAHNHPSGDPTPSREDIEL 83 (113)
T ss_pred hhheEEEEeeCCCCCCCCCHHHHHH
Confidence 4678999999999999999999875
No 39
>PF14220 DUF4329: Domain of unknown function (DUF4329)
Probab=31.66 E-value=41 Score=28.99 Aligned_cols=65 Identities=20% Similarity=0.273 Sum_probs=36.8
Q ss_pred CCCceeEEEeeeEecCCeEEEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCCCCceEEEEecCCCC-----CCc
Q 018129 80 GGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAVGWYHSHPGY-----GCW 154 (360)
Q Consensus 80 ~~p~EV~GlLLG~~~~~~leVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~~e~vVGWYHSHP~~-----g~~ 154 (360)
....|.||+. |+..++.+.-| -|..+....+..... . .-.+..+|+-||||..+ +-.
T Consensus 18 ~~nrEy~G~I-~~~~~G~y~~t----~p~~G~~~~~~~~~~--~-----------~p~g~~~vA~yHTHG~~~~~y~~ev 79 (123)
T PF14220_consen 18 RENREYCGYI-GKDEDGKYFAT----EPRRGENASCYPSNP--P-----------CPNGSTIVASYHTHGAYSDGYDNEV 79 (123)
T ss_pred cCCcEEEEEE-EEcCCCcEEee----cCccCCCCCcCCCCc--c-----------cccccceeeEeecccccCCCccccC
Confidence 3578999987 45555554333 244443322222110 0 01246899999999865 346
Q ss_pred cCHHhHHH
Q 018129 155 LSGIDVST 162 (360)
Q Consensus 155 ~S~iDI~t 162 (360)
+|..|+..
T Consensus 80 fS~~D~~~ 87 (123)
T PF14220_consen 80 FSPQDIRG 87 (123)
T ss_pred CCHHHhhh
Confidence 77777754
No 40
>PF14778 ODR4-like: Olfactory receptor 4-like
Probab=30.89 E-value=78 Score=31.98 Aligned_cols=61 Identities=20% Similarity=0.237 Sum_probs=38.2
Q ss_pred EEeeeEe-cCCeEEEEEEEeCCcccCCCc---cc--------cccC-hHHHHHHHHHHHHHhCCCCceEEEEecCCC
Q 018129 87 GLMQGKT-DGDAIIVMDAFALPVEGTETR---VN--------AQAD-AYEYMVDYSQTNKQAGRLENAVGWYHSHPG 150 (360)
Q Consensus 87 GlLLG~~-~~~~leVtd~F~lP~~~te~~---v~--------~~~e-~~ey~~~ml~~~r~v~~~e~vVGWYHSHP~ 150 (360)
|+|+|.. ..+.-.|-+..+.|.+.++.. +. ++.+ ..++..+..|++ --|..|||.|-.+|.
T Consensus 1 GLlIGq~~s~~kd~Vv~l~~tP~~d~~~~~~~~~~~~~~~~~id~~WVaeHA~qVsRML---PGGi~VlGifvv~~~ 74 (362)
T PF14778_consen 1 GLLIGQSSSSQKDYVVHLARTPPEDTDDEESDVRTSDSSIKDIDEEWVAEHARQVSRML---PGGISVLGIFVVAPD 74 (362)
T ss_pred CeEeccccCCCcceEEEecCCCCccccccccccccccccccccCHHHHHHHHHHHHhhC---CCCcEEEEEEEEcCH
Confidence 8999998 666667888888887654433 00 1111 123444444443 347999999987763
No 41
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=30.76 E-value=67 Score=37.67 Aligned_cols=109 Identities=17% Similarity=0.256 Sum_probs=66.5
Q ss_pred CCCceeEEEeeeEecCC---eEEEEEEEeCCcccCCCcccccc-ChHHHHHHHHHHHHHhCCCCceEEEEecCCCCCCcc
Q 018129 80 GGTIEVMGLMQGKTDGD---AIIVMDAFALPVEGTETRVNAQA-DAYEYMVDYSQTNKQAGRLENAVGWYHSHPGYGCWL 155 (360)
Q Consensus 80 ~~p~EV~GlLLG~~~~~---~leVtd~F~lP~~~te~~v~~~~-e~~ey~~~ml~~~r~v~~~e~vVGWYHSHP~~g~~~ 155 (360)
.....|.|++.|+-..+ .-+|...--+|+-+.-..|.... -+.+ + - --.++.++||-|+..+-=+++
T Consensus 2151 D~~vqvag~vyG~s~~d~p~ikeI~~~~lVPQlgs~~~vq~~s~vP~d-------l-p-~~e~le~lGwihtq~~el~~l 2221 (2365)
T COG5178 2151 DPHVQVAGLVYGKSGSDNPQIKEILSFGLVPQLGSLSGVQSSSFVPHD-------L-P-GDEDLEILGWIHTQDDELPYL 2221 (2365)
T ss_pred ccceeeEEEEeccCCccCcchhheeEEEeeccccccccccccccCCCC-------C-C-CcccceeeEEEecCCcccchh
Confidence 34578999999976422 34555444568765433332211 0000 0 0 013578999999998877888
Q ss_pred CHHhHHHHHhhhhcCCC--eEEEEEcCCCCccCCeeeEEEEEEccCCCC
Q 018129 156 SGIDVSTQMLNQQFQEP--FLAVVIDPTRTVSAGKVEIGAFRTYPEGYK 202 (360)
Q Consensus 156 S~iDI~tQ~~yQ~~~~p--~V~LVvDp~~t~~~G~v~ikAFRl~p~~~~ 202 (360)
+..++.++.. --..+. +|-|.|.- -.|.++++||.+..+|+.
T Consensus 2222 ~~~~v~th~k-~~~d~~~d~v~ltv~~----~pgsiSl~ay~v~keG~~ 2265 (2365)
T COG5178 2222 EVAGVLTHRK-KIVDPEWDAVTLTVSY----LPGSISLRAYVVKKEGCN 2265 (2365)
T ss_pred hhhhhhhhhh-cccCccccceeeeeee----ccceeeeeeeeehhcccc
Confidence 9888887642 112233 34444442 278999999999988875
No 42
>COG1029 FwdB Formylmethanofuran dehydrogenase subunit B [Energy production and conversion]
Probab=30.56 E-value=1.6e+02 Score=30.37 Aligned_cols=57 Identities=28% Similarity=0.465 Sum_probs=33.5
Q ss_pred hCCCCceEEE----EecCCC----CCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEcc
Q 018129 135 AGRLENAVGW----YHSHPG----YGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYP 198 (360)
Q Consensus 135 v~~~e~vVGW----YHSHP~----~g~~~S~iDI~tQ~~yQ~~~~p~V~LVvDp~~t~~~G~v~ikAFRl~p 198 (360)
.||...+|=| +||||. |+.||-+.-. ++-...--.|+|||.+|. .-++.=-.+++-|
T Consensus 138 KNraDviVyWGtNP~~shPRhmSRYs~f~RG~~~------~rGr~dRtvIvVD~RkT~-TAklad~~~qi~p 202 (429)
T COG1029 138 KNRADVIVYWGTNPMHSHPRHMSRYSVFPRGFFR------PRGREDRTVIVVDPRKTA-TAKLADNHVQIKP 202 (429)
T ss_pred cccccEEEEeCCCcccccchhhhhcccccccccc------cCCcccceEEEEecCcCc-hhhhhhheEecCC
Confidence 4677888888 899995 4455554311 122233467999998874 3343322344433
No 43
>PF15659 Toxin-JAB1: JAB-like toxin 1
Probab=26.69 E-value=70 Score=29.03 Aligned_cols=27 Identities=26% Similarity=0.299 Sum_probs=21.8
Q ss_pred hCCCCceEEEEecCCCCCCccCHHhHHH
Q 018129 135 AGRLENAVGWYHSHPGYGCWLSGIDVST 162 (360)
Q Consensus 135 v~~~e~vVGWYHSHP~~g~~~S~iDI~t 162 (360)
.+.+..++. .||||.....+|..|...
T Consensus 112 ~~~~~~iid-iHSHP~~~~~~S~~D~~~ 138 (162)
T PF15659_consen 112 KNNGNKIID-IHSHPENSNGPSGNDMKN 138 (162)
T ss_pred ccCCceEEE-eccCCCCCCCCCcchhhh
Confidence 356678888 999997777999988765
No 44
>PF04002 RadC: RadC-like JAB domain; InterPro: IPR001405 This family was named initially with reference to the Escherichia coli radC102 mutation which suggested that RadC was involved in repair of DNA lesions []. However the relevant mutation has subsequently been shown to be in recG, not radC []. In addition all attempts to characterise a radiation-related function for RadC in Streptococcus pneumoniae failed, suggesting that it is not involved in repair of DNA lesions, in recombination during transformation, in gene conversion, nor in mismatch repair [].; PDB: 2QLC_A.
Probab=25.96 E-value=4e+02 Score=22.42 Aligned_cols=83 Identities=16% Similarity=0.043 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHhcCCCceeEEEeeeEecCCeE-EEEEEEeCCcccCCCccccccChHHHHHHHHHHHHHhCCCCceEEEE
Q 018129 67 ALALLKMVVHARSGGTIEVMGLMQGKTDGDAI-IVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAVGWY 145 (360)
Q Consensus 67 ~~vLlkIl~Ha~~~~p~EV~GlLLG~~~~~~l-eVtd~F~lP~~~te~~v~~~~e~~ey~~~ml~~~r~v~~~e~vVGWY 145 (360)
+..+...++....+.+.|++-++. ....+.+ .+...+ .|+-+++.+ ++.+ +++.+-.. +..-|=..
T Consensus 5 ~~~v~~~l~~~l~~~~~E~~~~l~-Ld~~~~li~~~~v~----~G~~~~~~v--~~R~----I~~~al~~--~A~~vIl~ 71 (123)
T PF04002_consen 5 PEDVADYLRPKLQGLDQEQFRVLY-LDSKNRLIGDEVVS----EGTIDSAPV--DPRE----IFRRALRL--NASSVILA 71 (123)
T ss_dssp HHHHHHHHTTTSS-TTS-EEEEEE-E-TTSBEEEEEEEE----ESTT-GGGC--SHHH----HHHHHHHT--T-SEEEEE
T ss_pred HHHHHHHHHHHhCCCCCeEEEEEE-ECCCCcEEEEEEec----ccCCCcccc--cHHH----HHHHHHhh--CCceEEEE
Confidence 344455555444445566666554 2233332 222222 344444433 2323 33333222 34556678
Q ss_pred ecCCCCCCccCHHhHHH
Q 018129 146 HSHPGYGCWLSGIDVST 162 (360)
Q Consensus 146 HSHP~~g~~~S~iDI~t 162 (360)
|-||+..+.||.-|+..
T Consensus 72 HNHPsG~~~PS~~D~~~ 88 (123)
T PF04002_consen 72 HNHPSGDPEPSDADIAL 88 (123)
T ss_dssp EE-TTS--S--HHHHHH
T ss_pred EEcCCCCCCCCHhHHHH
Confidence 99999999999999864
No 45
>PF06442 DHFR_2: R67 dihydrofolate reductase; InterPro: IPR009159 Dihydrofolate reductase (DHFR) (1.5.1.3 from EC) catalyses the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate, an essential step in de novo synthesis both of glycine and of purines and deoxythymidine phosphate (the precursors of DNA synthesis) [], and important also in the conversion of deoxyuridine monophosphate to deoxythymidine monophosphate. Although DHFR is found ubiquitously in prokaryotes and eukaryotes, and is found in all dividing cells, maintaining levels of fully reduced folate coenzymes, the catabolic steps are still not well understood []. Bacterial species possesses distinct DHFR enzymes (based on their pattern of binding diaminoheterocyclic molecules), but mammalian DHFRs are highly similar []. The active site is situated in the N-terminal half of the sequence, which includes a conserved Pro-Trp dipeptide; the tryptophan has been shown [] to be involved in the binding of substrate by the enzyme. Its central role in DNA precursor synthesis, coupled with its inhibition by antagonists such as trimethoprim and methotrexate, which are used as anti-bacterial or anti-cancer agents, has made DHFR a target of anticancer chemotherapy. However, resistance has developed against some drugs, as a result of changes in DHFR itself []. This entry represents a plasmid-encoded DHFR which shows a high level of resistance to the antibiotic trimethoprim. It is a homotetramer with an unusual pore, which contains the active site, passing through the middle of the molecule []. Its structure is unrelated to that of chromosomal DHFRs.; GO: 0004146 dihydrofolate reductase activity, 0042493 response to drug, 0055114 oxidation-reduction process; PDB: 1VIF_A 3SFM_A 2P4T_A 2GQV_A 2RK2_A 2RH2_A 2RK1_A 1VIE_A.
Probab=25.42 E-value=36 Score=26.37 Aligned_cols=11 Identities=36% Similarity=0.924 Sum_probs=7.0
Q ss_pred CceEEEEecCC
Q 018129 139 ENAVGWYHSHP 149 (360)
Q Consensus 139 e~vVGWYHSHP 149 (360)
-.|||||.+.-
T Consensus 40 g~vvgwy~t~l 50 (78)
T PF06442_consen 40 GQVVGWYCTKL 50 (78)
T ss_dssp EEEEEEE--SS
T ss_pred ceEeEEEeccc
Confidence 47999997653
Done!